Diagenode

DNA shearing

417 publications found.

DNA fragmentation and quality control analysis
Published: September, 2016

Abstract: Optimal data generation using NGS platforms relies on a few sample-preparation prerequisites, namely, precise DNA fragmentation, size-range analysis, and smear quantification. The Diagenode One, Bioruptor®, Megaruptor®, and Fragment A...
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Acetylation of intragenic histones on HPV16 correlates with enhanced HPV16 gene expression.
Published: August, 2015

Abstract: We report that many histone modifications are unevenly distributed over the HPV16 genome in cervical cancer cells as well as in HPV16-immortalized keratinocytes. For example, H3K36me3 and H3K9Ac that are common in highly expressed cellular genes a...
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Concurrent whole-genome haplotyping and copy-number profiling of single cells.
Published: June, 2015

Abstract: Methods for haplotyping and DNA copy-number typing of single cells are paramount for studying genomic heterogeneity and enabling genetic diagnosis. Before analyzing the DNA of a single cell by microarray or next-generation sequencing, a whole-geno...
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Gene chip analysis of Arabidopsis thaliana genomic DNA methylation and gene expression in response to carbendazim.
Published: June, 2015

Abstract: OBJECTIVES: To examine the effects of carbendazim on Arabidopsis genomic DNA methylation and gene expression. RESULTS: Carbendazim caused widespread changes in gene loci methylation and gene expression. With 0.1 mM (D2) and 0.2 mM (D3) carbendazim...
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Characterization of genome-wide ordered sequence-tagged Mycobacterium mutant libraries by Cartesian Pooling-Coordinate Sequencing.
Published: May, 2015

Abstract: Reverse genetics research approaches require the availability of methods to rapidly generate specific mutants. Alternatively, where these methods are lacking, the construction of pre-characterized libraries of mutants can be extremely valuable. Ho...
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Within-host diversity of MRSA antimicrobial resistances.
Published: May, 2015

Abstract: OBJECTIVES: MRSA is a major antimicrobial resistance (AMR) pathogen. The reservoir of infecting isolates is colonization, which is the site of evolutionary selection. The aim was to identify if AMRs in colonizing MRSA populations diversified and p...
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A genomewide catalogue of single nucleotide polymorphisms in white-beaked and Atlantic white-sided dolphins
Published: May, 2015

Abstract: The field of population genetics is rapidly moving into population genomics as the quantity of data generated by high-throughput sequencing platforms increases. In this study, we used restriction-site-associated DNA sequencing (RADSeq) to recover ...
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Development of microsatellite primers in the protected species Viola elatior (Violaceae) using next-generation sequencing.
Published: May, 2015

Abstract: PREMISE OF THE STUDY: Viola elatior (Violaceae) is a Eurasian perennial plant species in which French populations are threatened by anthropogenic pressures. Microsatellite primers were developed to investigate its genetic structure and diversity. ...
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Th17 cells transdifferentiate into regulatory T cells during resolution of inflammation.
Published: April, 2015

Abstract: Inflammation is a beneficial host response to infection but can contribute to inflammatory disease if unregulated. The Th17 lineage of T helper (Th) cells can cause severe human inflammatory diseases. These cells exhibit both instability (they can...
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Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement.
Published: April, 2015

Abstract: Upland cotton is a model for polyploid crop domestication and transgenic improvement. Here we sequenced the allotetraploid Gossypium hirsutum L. acc. TM-1 genome by integrating whole-genome shotgun reads, bacterial artificial chromosome (BAC)-end ...
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High-throughput and quantitative assessment of enhancer activity in mammals by CapStarr-seq.
Published: April, 2015

Abstract: Cell-type specific regulation of gene expression requires the activation of promoters by distal genomic elements defined as enhancers. The identification and the characterization of enhancers are challenging in mammals due to their genome complexi...
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Draft genome sequences of 26 porphyromonas strains isolated from the canine oral microbiome.
Published: April, 2015

Abstract: We present the draft genome sequences for 26 strains of Porphyromonas (P. canoris, P. gulae, P. cangingavalis, P. macacae, and 7 unidentified) and an unidentified member of the Porphyromonadaceae family. All of these strains were isolated from the...
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Phylogenomic analysis shows that Bacillus amyloliquefaciens subsp plantarum is a later heterotypic synonym of Bacillus methylotrophicus.
Published: April, 2015

Abstract: The rhizosphere isolated bacteria belonging to the Bacillus amyloliquefaciens subsp. plantarum and Bacillus methylotrophicus clades are an important group of strains that are used as plant growth promoters and antagonists of plant pathogens. These...
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Resolving phylogenetic relationships of the recently radiated carnivorous plant genus Sarracenia using target enrichment.
Published: April, 2015

Abstract: The North American carnivorous pitcher plant genus Sarracenia (Sarraceniaceae) is a relatively young clade (
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Enrichment of an intraspecific genetic map of upland cotton by developing markers using parental RAD sequencing.
Published: April, 2015

Abstract: RAD sequencing was performed using DH962 and Jimian5 as upland cotton mapping parents. Sequencing data for DH962 and Jimian5 were assembled into the genome sequences of ≈55.27 and ≈57.06 Mb, respectively. Analysing genome sequences of the two pare...
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5-hydroxymethylcytosine marks promoters in colon that resist DNA hypermethylation in cancer.
Published: April, 2015

Abstract: BACKGROUND: The discovery of cytosine hydroxymethylation (5hmC) as a mechanism that potentially controls DNA methylation changes typical of neoplasia prompted us to investigate its behaviour in colon cancer. 5hmC is globally reduced in proliferati...
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Mitogenomic phylogeny of the common long-tailed macaque (Macaca fascicularis fascicularis).
Published: March, 2015

Abstract: BACKGROUND: Long-tailed macaques (Macaca fascicularis) are an important model species in biomedical research and reliable knowledge about their evolutionary history is essential for biomedical inferences. Ten subspecies have been recognized, of wh...
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Polyploidy can drive rapid adaptation in yeast.
Published: March, 2015

Abstract: Polyploidy is observed across the tree of life, yet its influence on evolution remains incompletely understood. Polyploidy, usually whole-genome duplication, is proposed to alter the rate of evolutionary adaptation. This could occur through comple...
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Evolution of the bamboos (Bambusoideae; Poaceae): a full plastome phylogenomic analysis.
Published: March, 2015

Abstract: BACKGROUND: Bambusoideae (Poaceae) comprise three distinct and well-supported lineages: tropical woody bamboos (Bambuseae), temperate woody bamboos (Arundinarieae) and herbaceous bamboos (Olyreae). Phylogenetic studies using chloroplast markers ha...
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Breeding scheme and maternal small RNAs affect the efficiency of transgenerational inheritance of a paramutation in mice.
Published: March, 2015

Abstract: Paramutations result from interactions between two alleles at a single locus, whereby one induces a heritable change in the other. Although common in plants, paramutations are rarely studied in animals. Here, we report a new paramutation mouse mod...
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Genome-wide mapping reveals conservation of promoter DNA methylation following chicken domestication.
Published: March, 2015

Abstract: It is well-known that environment influences DNA methylation, however, the extent of heritable DNA methylation variation following animal domestication remains largely unknown. Using meDIP-chip we mapped the promoter methylomes for 23,316 genes in...
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Population differentiation determined from putative neutral and divergent adaptive genetic markers in Eulachon (Thaleichthys pacificus, Osmeridae), an anadromous Pacific smelt.
Published: March, 2015

Abstract: Twelve eulachon (Thaleichthys pacificus, Osmeridae) populations ranging from Cook Inlet, Alaska and along the west coast of North America to the Columbia River were examined by restriction-site-associated DNA (RAD) sequencing to elucidate patterns...
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Functional characterization of IgA-targeted bacterial taxa from undernourished Malawian children that produce diet-dependent enteropathy
Published: February, 2015

Abstract: To gain insights into the interrelationships among childhood undernutrition, the gut microbiota, and gut mu- cosal immune/barrier function, we purified bacterial strains targeted by immunoglobulin A (IgA) from the fecal microbiota of two cohorts o...
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Genome-wide profiling of DNA methylation provides insights into epigenetic regulation of fungal development in a plant pathogenic fungus, Magnaporthe oryzae.
Published: February, 2015

Abstract: DNA methylation is an important epigenetic modification that regulates development of plants and mammals. To investigate the roles of DNA methylation in fungal development, we profiled genome-wide methylation patterns at single-nucleotide resoluti...
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Intermediate DNA methylation is a conserved signature of genome regulation.
Published: February, 2015

Abstract: The role of intermediate methylation states in DNA is unclear. Here, to comprehensively identify regions of intermediate methylation and their quantitative relationship with gene activity, we apply integrative and comparative epigenomics to 25 hum...
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Epigenetic and transcriptional determinants of the human breast.
Published: February, 2015

Abstract: While significant effort has been dedicated to the characterization of epigenetic changes associated with prenatal differentiation, relatively little is known about the epigenetic changes that accompany post-natal differentiation where fully funct...
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Phylogenomics of Phrynosomatid Lizards: Conflicting Signals from Sequence Capture versus Restriction Site Associated DNA Sequencing
Published: February, 2015

Abstract: Sequence capture and restriction site associated DNA sequencing (RADseq) are popular methods for obtaining large numbers of loci for phylogenetic analysis. These methods are typically used to collect data at different evolutionary timescales; sequ...
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Circulating nucleic acids damage DNA of healthy cells by integrating into their genomes
Published: February, 2015

Abstract: Whether nucleic acids that circulate in blood have any patho-physiological functions in the host have not been explored.We report here that far from being inert molecules, circulating nucleic acids have significant biological activities of their o...
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Single-Base Resolution Analysis of 5-Formyl and 5-Carboxyl Cytosine Reveals Promoter DNA Methylation Dynamics.
Published: February, 2015

Abstract: Ten eleven translocation (Tet) proteins oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). 5fC and 5caC can be further excised by thymine-DNA glycosylase (Tdg). Here, we present...
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Curcumin inhibits anchorage-independent growth of HT29 human colon cancer cells by targeting epigenetic restoration of the tumor suppressor gene DLEC1.
Published: January, 2015

Abstract: Colorectal cancer remains the most prevalent malignancy in humans. The impact of epigenetic alterations on the development of this complex disease is now being recognized. The dynamic and reversible nature of epigenetic modifications makes them a ...
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Age dependent changes in the LPS induced transcriptome of bovine dermal fibroblasts occurs without major changes in the methylome.
Published: January, 2015

Abstract: BackgroundBy comparing fibroblasts collected from animals at 5-months or 16-months of age we have previously found that the cultures from older animals produce much more IL-8 in response to lipopolysaccharide (LPS) stimulation. We now expand this ...
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Genome-wide DNA methylation analysis in Graves' disease.
Published: January, 2015

Abstract: As an autoimmune disease, Graves' disease (GD) is associated with many genetic and environmental risk factors. Although the exact mechanism remains unclear, epigenetic determinants, such as DNA methylation, are thought to contribute to the pathoge...
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Recurrent ETNK1 mutations in atypical chronic myeloid leukemia.
Published: January, 2015

Abstract: Despite the recent identification of recurrent SETBP1 mutations in atypical chronic myeloid leukemia (aCML), a complete description of the somatic lesions responsible for the onset of this disorder is still lacking. To find additional somatic abno...
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Genetic evidence for ecological divergence in kokanee salmon.
Published: January, 2015

Abstract: The evolution of locally adapted phenotypes among populations that experience divergent selective pressures is a central mechanism for generating and maintaining biodiversity. Recently, the advent of high-throughput DNA sequencing technology has p...
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Genome-wide methylation analysis in Silver-Russell syndrome patients.
Published: January, 2015

Abstract: Silver-Russell syndrome (SRS) is a clinically heterogeneous disorder characterised by severe in utero growth restriction and poor postnatal growth, body asymmetry, irregular craniofacial features and several additional minor malformations. The aet...
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The human urine virome in association with urinary tract infections
Published: January, 2015

Abstract: While once believed to represent a sterile environment, the human urinary tract harbors a unique cellular microbiota. We sought to determine whether the human urinary tract also is home to viral communities whose membership might reflect urinary t...
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Amplification of pico-scale DNA mediated by bacterial carrier DNA for small-cell-number transcription factor ChIP-seq.
Published: January, 2015

Abstract: BACKGROUND: Chromatin-Immunoprecipitation coupled with deep sequencing (ChIP-seq) is used to map transcription factor occupancy and generate epigenetic profiles genome-wide. The requirement of nano-scale ChIP DNA for generation of sequencing libra...
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Trichoderma reesei meiosis generates segmentally aneuploid progeny with higher xylanase-producing capability.
Published: January, 2015

Abstract: BACKGROUND: Hypocrea jecorina is the sexual form of the industrial workhorse fungus Trichoderma reesei that secretes cellulases and hemicellulases to degrade lignocellulosic biomass into simple sugars, such as glucose and xylose. H. jecorina CBS99...
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CpG signalling, H2A.Z/H3 acetylation and microRNA-mediated deferred self-attenuation orchestrate foetal NOS3 expression.
Published: January, 2015

Abstract: BACKGROUND: An adverse intrauterine environment leads to permanent physiological changes including vascular tone regulation, potentially influencing the risk for adult vascular diseases. We therefore aimed to monitor responsive NOS3 expression in ...
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Molecular Analysis of a Recurrent Sarcoma Identifies a Mutation in FAF1.
Published: January, 2015

Abstract: A patient presented with a recurrent sarcoma (diagnosed as leiomyosarcoma) 12 years after the removal of an initial cancer (diagnosed as extracompartmental osteosarcoma) distally on the same limb. Following surgery, the sarcoma and unaffected musc...
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Locus-specific DNA methylation analysis of retrotransposons in ES, somatic and cancer cells using High-Throughput Targeted Repeat Element Bisulfite Sequencing
Published: January, 2015

Abstract: DNA methylation is a major epigenetic mark associated with multiple aspects of retrotransposons within the mammalian genome. In order to study DNA methylation of a large number of retrotransposons on an individual-locus basis, we have developed a ...
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Sequencing, identification and mapping of primed L1 elements (SIMPLE) reveals significant variation in full length L1 elements between individuals.
Published: January, 2015

Abstract: BACKGROUND: There are over a half a million copies of L1 retroelements in the human genome which are responsible for as much as 0.5% of new human genetic diseases. Most new L1 inserts arise from young source elements that are polymorphic in the hu...
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Molecular and Biochemical Characterization of a Novel Multidomain Xylanase from Arthrobacter sp. GN16 Isolated from the Feces of Grus nigricollis.
Published: January, 2015

Abstract: A novel glycosyl hydrolase family 10 (GH 10) xylanase (XynAGN16), consisting of five domains, was revealed from the genome sequence of Arthrobacter sp. GN16 isolated from the feces of Grus nigricollis. XynAGN16 and its truncated derivatives XynAGN...
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DNA Methylation Analysis of the Macrosatellite Repeat Associated with FSHD Muscular Dystrophy at Single Nucleotide Level.
Published: December, 2014

Abstract: Facioscapulohumeral muscular dystrophy (FSHD) is one of the most common inherited diseases of the skeletal muscle. It is characterized by asymmetric muscle weakness and variable penetrance. FSHD is linked to a reduction in copy number of the D4Z4 ...
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Epigenetic modification of the PD-1 (Pdcd1) promoter in effector CD4(+) T cells tolerized by peptide immunotherapy.
Published: December, 2014

Abstract: Clinically effective antigen-based immunotherapy must silence antigen-experienced effector T cells (Teff) driving ongoing immune pathology. Using CD4(+) autoimmune Teff cells, we demonstrate that peptide immunotherapy (PIT) is strictly dependent u...
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Whole-exome sequencing identify a new mutation of MYH7 in a Chinese family with left ventricular noncompaction.
Published: December, 2014

Abstract: BACKGROUND: Left ventricular noncompaction (LVNC) is a genetic cardiomyopathy results from the failure of myocardial development during embryogenesis. Previous reports show that defects in TAZ, SCN5A, TPM1, YWHAE, MYH7, ACTC1 and TNNT2 are associa...
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Next-generation sequencing workflow for assembly of non-model mitogenomes exemplified with North Pacific Albatrosses (Phoebastria spp.).
Published: December, 2014

Abstract: Use of complete mitochondrial genomes (mitogenomes) can greatly increase the resolution achievable in phylogeographic and historical demographic studies. Using next generation sequencing methods, it is now feasible to efficiently sequence mitogeno...
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Cold acclimation induces distinctive changes in the chromatin state and transcript levels of COR genes in Cannabis sativa varieties with contrasting cold acclimation capacities.
Published: December, 2014

Abstract: Little is known about the capacity of Cannabis sativa to cold acclimate and develop freezing tolerance. This study investigates the cold acclimation capacity of nine C. sativa varieties and the underlying genetic and epigenetic responses. The vari...
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Frequency and phenotypic spectrum of germline mutations in POLE and seven other polymerase genes in 266 patients with colorectal adenomas and carcinomas.
Published: December, 2014

Abstract: In a number of families with colorectal adenomatous polyposis or suspected Lynch syndrome / HNPCC, no germline alteration in the APC, MUTYH, or mismatch repair (MMR) genes are found. Missense mutations in the polymerase genes POLE and POLD1 have r...
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Plasmid Flux in Escherichia coli ST131 Sublineages, Analyzed by Plasmid Constellation Network (PLACNET), a New Method for Plasmid Reconstruction from Whole Genome Sequences.
Published: December, 2014

Abstract: Bacterial whole genome sequence (WGS) methods are rapidly overtaking classical sequence analysis. Many bacterial sequencing projects focus on mobilome changes, since macroevolutionary events, such as the acquisition or loss of mobile genetic eleme...
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The maize brown midrib4 (bm4) gene encodes a functional folylpolyglutamate synthase (FPGS).
Published: December, 2014

Abstract: Mutations in the brown midrib4 (bm4) gene affect the accumulation and composition of lignin in maize. Fine mapping analysis of bm4 narrowed the candidate region to an ~105 kb interval on chromosome 9 containing six genes. Only one of these six gen...
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Genomic evidence of geographically widespread effect of gene flow from polar bears into brown bears.
Published: December, 2014

Abstract: Polar bears are an arctic, marine adapted species that is closely related to brown bears. Genome analyses have shown that polar bears are distinct and genetically homogeneous in comparison to brown bears. However, these analyses have also revealed...
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Initiation of DNA replication from non-canonical sites on an origin-depleted chromosome.
Published: December, 2014

Abstract: Eukaryotic DNA replication initiates from multiple sites on each chromosome called replication origins (origins). In the budding yeast Saccharomyces cerevisiae, origins are defined at discrete sites. Regular spacing and diverse firing characterist...
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Genome-wide DNA methylation analysis in precursor B-cells.
Published: December, 2014

Abstract: DNA methylation is responsible for regulating gene expression and cellular differentiation and for maintaining genomic stability during normal human development. Furthermore, it plays a significant role in the regulation of hematopoiesis. In order...
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Evaluation of methods to detect CALR mutations in myeloproliferative neoplasms
Published: November, 2014

Abstract: The recent discovery of somatically acquired CALR mutations in a substantial proportion of patients with myeloproliferative neoplasms has provided a new marker of clonal disease, advancing both diagnosis and prognosis in these previously difficult...
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Epigenetic memory of the first cell fate decision prevents complete ES cell reprogramming into trophoblast.
Published: November, 2014

Abstract: Embryonic (ES) and trophoblast (TS) stem cells reflect the first, irrevocable cell fate decision in development that is reinforced by distinct epigenetic lineage barriers. Nonetheless, ES cells can seemingly acquire TS-like characteristics upon ma...
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Synergistic template-free synthesis of dsDNA by Thermococcus nautili primase PolpTN2, DNA polymerase PolB, and pTN2 helicase.
Published: November, 2014

Abstract: A combination of three enzymes from the hyperthermophilic archaeon Thermococcus nautili, DNA primase PolpTN2, DNA polymerase PolB, and pTN2 DNA helicase, was found to synthesize up to 300-400 ng/µl dsDNA from deoxynucleotide triphosphates in less ...
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Regulatory network decoded from epigenomes of surface ectoderm-derived cell types.
Published: November, 2014

Abstract: Developmental history shapes the epigenome and biological function of differentiated cells. Epigenomic patterns have been broadly attributed to the three embryonic germ layers. Here we investigate how developmental origin influences epigenomes. We...
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Single mutations in sasA enable a simpler ΔcikA gene network architecture with equivalent circadian properties.
Published: November, 2014

Abstract: The circadian input kinase of the cyanobacterium Synechococcus elongatus PCC 7942 (CikA) is important both for synchronizing circadian rhythms with external environmental cycles and for transferring temporal information between the oscillator and ...
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Combining MeDIP-seq and MRE-seq to investigate genome-wide CpG methylation.
Published: November, 2014

Abstract: DNA CpG methylation is a widespread epigenetic mark in high eukaryotes including mammals. DNA methylation plays key roles in diverse biological processes such as X chromosome inactivation, transposable element repression, genomic imprinting, and c...
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Heterochromatin-mediated gene silencing facilitates the diversification of olfactory neurons.
Published: November, 2014

Abstract: An astounding property of the nervous system is its cellular diversity. This diversity, which was initially realized by morphological and electrophysiological differences, is ultimately produced by variations in gene-expression programs. In most c...
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A phylogenomic analysis of turtles.
Published: November, 2014

Abstract: Molecular analyses of turtle relationships have overturned prevailing morphological hypotheses and prompted the development of a new taxonomy. Here we provide the first genome-scale analysis of turtle phylogeny. We sequenced 2381 ultraconserved el...
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Characterization of microsatellite markers for pinedrops, Pterospora andromedea (Ericaceae), from Illumina MiSeq sequencing.
Published: November, 2014

Abstract: UNLABELLED: • PREMISE OF THE STUDY: Pterospora andromedea (Ericaceae) is a mycoheterotrophic plant endemic to North America with a disjunct distribution. Eastern populations are in decline compared to western populations. Microsatellite loci will ...
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Genome-wide identification of aberrantly methylated promoters in ovarian tissue of prenatally androgenized rats.
Published: November, 2014

Abstract: OBJECTIVE: To identify aberrantly methylated candidate genes that are involved in the development of polycystic ovary syndrome (PCOS). DESIGN: Animal model. SETTING: University-affiliated laboratory. ANIMAL(S): Sprague-Dawley rats. INTERVENTION(S)...
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Synthetic secondary chromosomes in Escherichia coli based on the replication origin of chromosome II in Vibrio cholerae.
Published: October, 2014

Abstract: Recent developments in DNA-assembly methods make the synthesis of synthetic chromosomes a reachable goal. However, the redesign of primary chromosomes bears high risks and still requires enormous resources. An alternative approach is the addition ...
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Next Generation Sequencing Identifies a Novel Rearrangement in the HBB Cluster Permitting to-the-Base Characterization
Published: October, 2014

Abstract: Genetic testing for hemoglobinopathies is required for prenatal diagnosis, understanding complex cases where multiple pathogenic variants may be present or investigating cases of unexplained anemia. Characterization of disease causing variants tha...
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RNaseH1 regulates TERRA-telomeric DNA hybrids and telomere maintenance in ALT tumour cells.
Published: October, 2014

Abstract: A fraction of cancer cells maintain telomeres through the telomerase-independent, 'Alternative Lengthening of Telomeres' (ALT) pathway. ALT relies on homologous recombination (HR) between telomeric sequences; yet, what makes ALT telomeres recombin...
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Prenatal stress-induced programming of genome-wide promoter DNA methylation in 5-HTT-deficient mice.
Published: October, 2014

Abstract: The serotonin transporter gene (5-HTT/SLC6A4)-linked polymorphic region has been suggested to have a modulatory role in mediating effects of early-life stress exposure on psychopathology rendering carriers of the low-expression short (s)-variant m...
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Sperm DNA Methylation Analysis in Swine Reveals Conserved and Species-Specific Methylation Patterns and Highlights an Altered Methylation at the GNAS Locus in Infertile Boars.
Published: October, 2014

Abstract: Male infertility is an increasing health issue in today's society, for both human or livestock populations. In livestock, male infertility slows the improvement of animal selection programs and agricultural productivity. There are increasing evide...
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MeDIP-on-Chip for Methylation Profiling
Published: October, 2014

Abstract: DNA methylation is an important regulatory step in gene expression. Knowledge of the alterations in DNA methylation at a whole genome scale improves our understanding of gene regulation and potential correlations with biological events or disease ...
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Notch signaling regulates myogenic regenerative capacity of murine and human mesoangioblasts.
Published: October, 2014

Abstract: Somatic stem cells hold attractive potential for the treatment of muscular dystrophies (MDs). Mesoangioblasts (MABs) constitute a myogenic subset of muscle pericytes and have been shown to efficiently regenerate dystrophic muscles in mice and dogs...
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Altered promoter nucleosome positioning is an early event in gene silencing.
Published: October, 2014

Abstract: Gene silencing in cancer frequently involves hypermethylation and dense nucleosome occupancy across promoter regions. How a promoter transitions to this silent state is unclear. Using colorectal adenomas, we investigated nucleosome positioning, DN...
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Retrotransposon-based profiling of mammalian epigenomes: DNA methylation of IAP LTRs in embryonic stem, somatic and cancer cells.
Published: September, 2014

Abstract: In the current study, we have used HT-TREBS to individually analyze the DNA methylation pattern of 4799 IAP LTR retrotransposons in embryonic stem, somatic and Neuro2A cells. According to the results, half of the loci within this family show const...
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Co-detection and sequencing of genes and transcripts from the same single cells facilitated by a microfluidics platform.
Published: September, 2014

Abstract: Despite the recent advance of single-cell gene expression analyses, co-measurement of both genomic and transcriptional signatures at the single-cell level has not been realized. However such analysis is necessary in order to accurately delineate h...
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5mC Oxidation by Tet2 Modulates Enhancer Activity and Timing of Transcriptome Reprogramming during Differentiation.
Published: September, 2014

Abstract: In mammals, cytosine methylation (5mC) is widely distributed throughout the genome but is notably depleted from active promoters and enhancers. While the role of DNA methylation in promoter silencing has been well documented, the function of this ...
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Epigenetic events determine tissue-specific toxicity of inhalational exposure to the genotoxic chemical 1,3-butadiene in male C57BL/6J mice
Published: September, 2014

Abstract: 1,3-Butadiene (BD), a widely used industrial chemical and a ubiquitous environmental pollutant, is a known human carcinogen. Although genotoxicity is an established mechanism of the tumorigenicity of BD, epigenetic effects have also been observed ...
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Asparagine synthetase deficiency detected by whole exome sequencing causes congenital microcephaly, epileptic encephalopathy and psychomotor delay.
Published: September, 2014

Abstract: Deficiency of Asparagine Synthetase (ASNSD, MIM 615574) is a very rare autosomal recessive disorder presenting with some brain abnormalities. Affected individuals have congenital microcephaly and progressive encephalopathy associated with severe i...
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Genome-wide CNV analysis in 221 unrelated patients and targeted high-throughput sequencing reveal novel causative candidate genes for colorectal adenomatous polyposis.
Published: September, 2014

Abstract: To uncover novel causative genes in patients with unexplained adenomatous polyposis, a model disease for colorectal cancer, we performed a genome-wide analysis of germline copy number variants (CNV) in a large, well characterized APC and MUTYH mut...
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Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera.
Published: September, 2014

Abstract: Gaining a genomic perspective on phylogeny requires the collection of data from many putatively independent loci across the genome. Among insects, an increasingly common approach to collecting this class of data involves transcriptome sequencing, ...
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A thermo-halo-tolerant and proteinase-resistant endoxylanase from Bacillus sp. HJ14.
Published: September, 2014

Abstract: A glycosyl hydrolase family 10 endoxylanase from Bacillus sp. HJ14 was grouped in a separated cluster with another six Bacillus endoxylanases which have not been characterized. These Bacillus endoxylanases showed less than 52% amino acid sequence ...
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Hypomethylated pollen bypasses the interploidy hybridization barrier in Arabidopsis.
Published: September, 2014

Abstract: Plants of different ploidy levels are separated by a strong postzygotic hybridization barrier that is established in the endosperm. Deregulated parent-of-origin specific genes cause the response to interploidy hybridizations, revealing an epigenet...
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Y chromosomes of 40% Chinese descend from three Neolithic super-grandfathers.
Published: August, 2014

Abstract: Demographic change of human populations is one of the central questions for delving into the past of human beings. To identify major population expansions related to male lineages, we sequenced 78 East Asian Y chromosomes at 3.9 Mbp of the non-rec...
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oxBS-450K: A method for analysing hydroxymethylation using 450K BeadChips.
Published: August, 2014

Abstract: DNA methylation analysis has become an integral part of biomedical research. For high-throughput applications such as epigenome-wide association studies, the Infinium HumanMethylation450 (450K) BeadChip is currently the platform of choice. However...
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Differences among brain tumor stem cell types and fetal neural stem cells in focal regions of histone modifications and DNA methylation, broad regions of modifications, and bivalent promoters.
Published: August, 2014

Abstract: BACKGROUND: Aberrational epigenetic marks are believed to play a major role in establishing the abnormal features of cancer cells. Rational use and development of drugs aimed at epigenetic processes requires an understanding of the range, extent, ...
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An improved method for including upper size range plasmids in metamobilomes.
Published: August, 2014

Abstract: Two recently developed isolation methods have shown promise when recovering pure community plasmid DNA (metamobilomes/plasmidomes), which is useful in conducting culture-independent investigations into plasmid ecology. However, both methods employ...
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Whole Exome Sequencing for Familial Bicuspid Aortic Valve Identifies Putative Variants.
Published: August, 2014

Abstract: BACKGROUND: -Bicuspid aortic valve (BAV) is the most common congenital cardiovascular malformation (CVM). Although highly heritable, few causal variants have been identified. The purpose of this study was to identify genetic variants underlying B...
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Source tracking of an anthrax outbreak in northeastern China using complete genome analysis and MLVA genotyping.
Published: July, 2014

Abstract: Anthrax is caused by Bacillus anthracis, an etiological agent behind zoonotic diseases worldwide. B. anthracis is also one of the most dangerous bioterrorism agents. An anthrax outbreak took place in Liaoning Province in northeastern China in Augu...
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DNA Break Mapping Reveals Topoisomerase II Activity Genome-Wide.
Published: July, 2014

Abstract: Genomic DNA is under constant assault by endogenous and exogenous DNA damaging agents. DNA breakage can represent a major threat to genome integrity but can also be necessary for genome function. Here we present approaches to map DNA double-strand...
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Homozygous missense variant in the human CNGA3 channel causes cone-rod dystrophy.
Published: July, 2014

Abstract: We assessed a large consanguineous Pakistani family (PKAB157) segregating early onset low vision problems. Funduscopic and electroretinographic evaluation of affected individuals revealed juvenile cone-rod dystrophy (CRD) with maculopathy. Other c...
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Genome-Wide Characterization of Light-Regulated Genes in Neurospora crassa.
Published: July, 2014

Abstract: The filamentous fungus Neurospora crassa responds to light in complex ways. To thoroughly study the transcriptional response of this organism to light, RNA-seq was used to analyze capped and polyadenylated mRNA prepared from mycelium grown for 24 ...
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Activating germline mutations in STAT3 cause early-onset multi-organ autoimmune disease.
Published: July, 2014

Abstract: Monogenic causes of autoimmunity provide key insights into the complex regulation of the immune system. We report a new monogenic cause of autoimmunity resulting from de novo germline activating STAT3 mutations in five individuals with a spectrum ...
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Genomic organization and evolution of double minutes/homogeneously staining regions with MYC amplification in human cancer.
Published: July, 2014

Abstract: The mechanism for generating double minutes chromosomes (dmin) and homogeneously staining regions (hsr) in cancer is still poorly understood. Through an integrated approach combining next-generation sequencing, single nucleotide polymorphism array...
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Comparative genome sequencing reveals chemotype-specific gene clusters in the toxigenic black mold Stachybotrys
Published: July, 2014

Abstract: Background The fungal genus Stachybotrys produces several diverse toxins that affect human health. Its strains comprise two mutually-exclusive toxin chemotypes, one producing satratoxins, which are a subclass of trichothecenes, and the other prod...
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Microsatellite Primers for the Fungi Rhizopogon kretzerae and R. salebrosus (Rhizopogonaceae) from 454 Shotgun Pyrosequencing
Published: July, 2014

Abstract: PREMISE OF THE STUDY: Rhizopogon kretzerae and R. salebrosus (Rhizopogonaceae) are ectomycorrhizal fungi symbiotic with pines and the mycoheterotrophic plant Pterospora andromedea (Ericaceae). Microsatellite loci will allow population genetic stu...
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Very small deletions within the NESP55 gene in pseudohypoparathyroidism type 1b.
Published: July, 2014

Abstract: Pseudohypoparathyroidism (PHP) is caused by reduced expression of genes within the GNAS cluster, resulting in parathormone resistance. The cluster contains multiple imprinted transcripts, including the stimulatory G protein α subunit (Gs-α) and NE...
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Comparison of five different RNA sources to examine the lactating bovine mammary gland transcriptome using RNA-Sequencing.
Published: July, 2014

Abstract: The objective of this study was to examine five different sources of RNA, namely mammary gland tissue (MGT), milk somatic cells (SC), laser microdissected mammary epithelial cells (LCMEC), milk fat globules (MFG) and antibody-captured milk mammary...
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Four methods of preparing mRNA 5' end libraries using the illumina sequencing platform.
Published: July, 2014

Abstract: BACKGROUND: The 5' untranslated regions of mRNA play an important role in their translation. RESULTS: Here, we describe the development of four methods of profiling mRNA 5' ends using the Illumina sequencing platform; the first method utilizes S...
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Genome-wide analysis of DNA 5-hmC in peripheral blood of uremia by hMeDIP-chip.
Published: July, 2014

Abstract: Abstract Background: Treatment of uremia is now dominated by dialysis; in some cases, patients are treated with dialysis for decades, but overall outcomes are disappointing. A number of studies have confirmed the relevance of several experimental ...
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GENOME-WIDE SCREEN OF PROMOTER METHYLATION IDENTIFIES NOVEL MARKERS IN DIET-INDUCED OBESE MICE.
Published: July, 2014

Abstract: OBJECTIVE: To investigate the genome-wide promoter methylation and gene expression for the identification of methylation markers in obesity. METHODS: Using a high-fat, diet-induced obese mouse model, we performed comprehensive DNA methylation prof...
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DNA topoisomerase 1α promotes transcriptional silencing of transposable elements through DNA methylation and histone lysine 9 dimethylation in Arabidopsis.
Published: July, 2014

Abstract: RNA-directed DNA methylation (RdDM) and histone H3 lysine 9 dimethylation (H3K9me2) are related transcriptional silencing mechanisms that target transposable elements (TEs) and repeats to maintain genome stability in plants. RdDM is mediated by sm...
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Characterization of bacteriophage communities and CRISPR profiles from dental plaque.
Published: June, 2014

Abstract: BACKGROUND: Dental plaque is home to a diverse and complex community of bacteria, but has generally been believed to be inhabited by relatively few viruses. We sampled the saliva and dental plaque from 4 healthy human subjects to determine whether...
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A role for migration-linked genes and genomic islands in divergence of a songbird.
Published: June, 2014

Abstract: Next-generation sequencing has made it possible to begin asking questions about the process of divergence at the level of the genome. For example, recently there has been a debate around the role of 'genomic islands of divergence' (i.e. blocks of ...
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Single-base-resolution methylomes of populus trichocarpa reveal the association between DNA methylation and drought stress
Published: June, 2014

Abstract: Background: DNA methylation is an important biological form of epigenetic modification, playing key roles in plant development and environmental responses. Results: In this study, we examined single-base resolution methylomes of Populus under cont...
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Transient accumulation of 5-carboxylcytosine indicates involvement of active demethylation in lineage specification of neural stem cells.
Published: June, 2014

Abstract: 5-Methylcytosine (5mC) is an epigenetic modification involved in regulation of gene activity during differentiation. Tet dioxygenases oxidize 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). Both 5fC an...
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Corolla Is a Novel Protein that Contributes to the Architecture of the Synaptonemal Complex of Drosophila.
Published: June, 2014

Abstract: In most organisms the synaptonemal complex (SC) connects paired homologs along their entire length during much of meiotic prophase. To better understand the structure of the SC, we aim to identify its components and to determine how each of these ...
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Conservation of streptococcal CRISPRs on human skin and saliva.
Published: June, 2014

Abstract: BACKGROUND: Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) are utilized by bacteria to resist encounters with their viruses. Human body surfaces have numerous bacteria that harbor CRISPRs, and their content can provide clues a...
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Deep sequencing reveals new aspects of progesterone receptor signaling in breast cancer cells.
Published: June, 2014

Abstract: Despite the pleiotropic effects of the progesterone receptor in breast cancer, the molecular mechanisms in play remain largely unknown. To gain a global view of the PR-orchestrated networks, we used next-generation sequencing to determine the prog...
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Genome editing in the human malaria parasite Plasmodium falciparum using the CRISPR-Cas9 system.
Published: June, 2014

Abstract: Genome manipulation in the malaria parasite Plasmodium falciparum remains largely intractable and improved genomic tools are needed to further understand pathogenesis and drug resistance. We demonstrated the CRISPR-Cas9 system for use in P. falcip...
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New lung cancer panel for high-throughput targeted resequencing.
Published: June, 2014

Abstract: We present a new next-generation sequencing-based method to identify somatic mutations of lung cancer. It is a comprehensive mutation profiling protocol to detect somatic mutations in 30 genes found frequently in lung adenocarcinoma. The total len...
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Phylogenomics of the plant family Araceae.
Published: June, 2014

Abstract: The biogeography, chromosome number evolution, pollination biology and evolutionary history of the plant family Araceae have recently become much clearer (Cabrera et al., 2008; Chartier et al., 2013; Cusimano et al., 2011, 2012; Nauheimer et al., ...
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Hydroxymethylation and DNA methylation profiles in the prefrontal cortex of the non-human primate rhesus macaque and the impact of maternal deprivation on hydroxymethylation.
Published: May, 2014

Abstract: 5-Hydroxymethylcytosine (5hmC) is abundant in the brain, suggesting an important role in epigenetic control of neuronal functions. In this paper, we show that 5hmC and 5-methylcytosine (5mC) levels are coordinately distributed in gene promoters of...
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A genome-wide analysis of Cas9 binding specificity using ChIP-seq and targeted sequence capture
Published: May, 2014

Abstract: Clustered regularly interspaced short palindromic repeat (CRISPR) RNA-guided nucleases have gathered considerable excitement as a tool for genome engineering. However, questions remain about the specificity of their target site recognition. Most p...
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Altered oral viral ecology in association with periodontal disease.
Published: May, 2014

Abstract: UNLABELLED: The human oral cavity is home to a large and diverse community of viruses that have yet to be characterized in patients with periodontal disease. We recruited and sampled saliva and oral biofilm from a cohort of humans either periodont...
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Discovery of transgene insertion sites by high throughput sequencing of mate pair libraries.
Published: May, 2014

Abstract: BACKGROUND: Transgenesis by random integration of a transgene into the genome of a zygote has become a reliable and powerful method for the creation of new mouse strains that express exogenous genes, including human disease genes, tissue specific ...
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Homeostatic maintenance of allele-specific p16 methylation in cancer cells accompanied by dynamic focal methylation and hydroxymethylation.
Published: May, 2014

Abstract: AIM: p16 Methylation frequently occurs in carcinogenesis. While it has been hypothesized that the p16 methylation states are dynamically maintained in cancer cells, direct evidence supporting this hypothesis has not been available until now. METHO...
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Massive gene amplification drives paediatric hepatocellular carcinoma caused by bile salt export pump deficiency.
Published: May, 2014

Abstract: Hepatocellular carcinoma (HCC) is almost invariably associated with an underlying inflammatory state, whose direct contribution to the acquisition of critical genomic changes is unclear. Here we map acquired genomic alterations in human and mouse ...
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Transmission from centenarians to their offspring of mtDNA heteroplasmy revealed by ultra-deep sequencing
Published: May, 2014

Abstract: The role that mtDNA heteroplasmy plays in healthy aging, familial longevity and the heritability patterns of low levels heteroplasmy in the elderly are largely unknown. We analyzed the low levels of mtDNA heteroplasmy in blood in a cohort of cente...
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Genomic analysis of the emergence of 20th century epidemic dysentery.
Published: May, 2014

Abstract: BACKGROUND: Shigella dysenteriae type 1 (Sd1) causes recurrent epidemics of dysentery associated with high mortality in many regions of the world. Sd1 infects humans at very low infectious doses (10 CFU), and treatment is complicated by the rapid ...
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Biogeography and phylogenomics of New World Bambusoideae (Poaceae), revisited.
Published: May, 2014

Abstract: • Premise of the study: New World Bambusoideae have only recently been studied in a phylogenomic context. Plastome sequences were determined and analyzed from Arundinaria appalachiana, A. tecta, and Olyra latifolia, to refine our knowledge of thei...
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EXPRSS: an Illumina based high-throughput expression-profiling method to reveal transcriptional dynamics.
Published: May, 2014

Abstract: BACKGROUND: Next Generation Sequencing technologies have facilitated differential gene expression analysis through RNA-seq and Tag-seq methods. RNA-seq has biases associated with transcript lengths, lacks uniform coverage of regions in mRNA and re...
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Reassessment of QTLs for Late Blight Resistance in the Tomato Accession L3708 Using a Restriction Site Associated DNA (RAD) Linkage Map and Highly Aggressive Isolates of Phytophthora infestans
Published: May, 2014

Abstract: omato late blight caused by the oomycete pathogen Phytophthora infestans (Mont.) de Bary is a major threat to tomato production in cool and wet environments. Intensified outbreaks of late blight have been observed globally from the 1980s, and are ...
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Function-based identification of mammalian enhancers using site-specific integration.
Published: May, 2014

Abstract: The accurate and comprehensive identification of functional regulatory sequences in mammalian genomes remains a major challenge. Here we describe site-specific integration fluorescence-activated cell sorting followed by sequencing (SIF-seq), an un...
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R-loops associated with triplet repeat expansions promote gene silencing in Friedreich ataxia and fragile X syndrome.
Published: May, 2014

Abstract: Friedreich ataxia (FRDA) and Fragile X syndrome (FXS) are among 40 diseases associated with expansion of repeated sequences (TREDs). Although their molecular pathology is not well understood, formation of repressive chromatin and unusual DNA struc...
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Early aberrant DNA methylation events in a mouse model of acute myeloid leukemia.
Published: April, 2014

Abstract: BACKGROUND: Aberrant DNA methylation is frequently found in human malignancies including acute myeloid leukemia (AML). While most studies focus on later disease stages, the onset of aberrant DNA methylation events and their dynamics during leukemi...
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Genome-Wide and Gene-Specific Epigenomic Platforms for Hepatocellular Carcinoma Biomarker Development Trials
Published: April, 2014

Abstract: The majority of the epigenomic reports in hepatocellular carcinoma have focused on identifying novel differentially methylated drivers or passengers of the oncogenic process. Few reports have considered the technologies in place for clinical trans...
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Epigenetic upregulation of corticotrophin-releasing hormone mediates postnatal maternal separation-induced memory deficiency.
Published: April, 2014

Abstract: Accumulating evidences demonstrated that early postnatal maternal separation induced remarkable social and memory defects in the adult rodents. Early-life stress induced long-lasting functional adaptation of neuroendocrine hypothalamic-pituitary-a...
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Whole Exome Sequencing Identifies Recessive PKHD1 Mutations in a Chinese Twin Family with Caroli Disease.
Published: April, 2014

Abstract: BACKGROUND: Mutations in PKHD1 cause autosomal recessive Caroli disease, which is a rare congenital disorder involving cystic dilatation of the intrahepatic bile ducts. However, the mutational spectrum of PKHD1 and the phenotype-genotype correlati...
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Folic acid stimulation of neural stem cell proliferation is associated with altered methylation profile of PI3K/Akt/CREB.
Published: April, 2014

Abstract: Proliferation of neural stem cells (NSCs) is required for development and repair in the nervous system. NSC amplification in vitro is a necessary step towards using NSC transplantation therapy to treat neurodegenerative diseases. Folic acid (FA) h...
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High-throughput sequencing exclusively identified a novel Torque teno virus genotype in serum of a patient with fatal fever.
Published: April, 2014

Abstract: Torque teno virus (TTV) has been found to be prevalent world-wide in healthy populations and in patients with various diseases, but its etiological role has not yet been determined. Using high-throughput unbiased sequencing to screen for viruses i...
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Frequent mutations in chromatin-remodelling genes in pulmonary carcinoids.
Published: March, 2014

Abstract: Pulmonary carcinoids are rare neuroendocrine tumours of the lung. The molecular alterations underlying the pathogenesis of these tumours have not been systematically studied so far. Here we perform gene copy number analysis (n=54), genome/exome (n...
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Disturbed subsurface microbial communities follow equivalent trajectories despite different structural starting points.
Published: March, 2014

Abstract: Microbial community structure, and niche and neutral processes can all influence response to disturbance. Here, we provide experimental evidence for niche versus neutral and founding community effects during a bioremediation-related organic carbon...
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Modelling mutational landscapes of human cancers in vitro.
Published: March, 2014

Abstract: Experimental models that recapitulate mutational landscapes of human cancers are needed to decipher the rapidly expanding data on human somatic mutations. We demonstrate that mutation patterns in immortalised cell lines derived from primary murine...
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Large-scale analysis of tandem repeat variability in the human genome.
Published: March, 2014

Abstract: Tandem repeats are short DNA sequences that are repeated head-to-tail with a propensity to be variable. They constitute a significant proportion of the human genome, also occurring within coding and regulatory regions. Variation in these repeats c...
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Fine mapping of genome activation in bovine embryos by RNA sequencing.
Published: March, 2014

Abstract: During maternal-to-embryonic transition control of embryonic development gradually switches from maternal RNAs and proteins stored in the oocyte to gene products generated after embryonic genome activation (EGA). Detailed insight into the onset of...
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Hook is an adapter that coordinates kinesin-3 and dynein cargo attachment on early endosomes.
Published: March, 2014

Abstract: Bidirectional membrane trafficking along microtubules is mediated by kinesin-1, kinesin-3, and dynein. Several organelle-bound adapters for kinesin-1 and dynein have been reported that orchestrate their opposing activity. However, the coordination...
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Sequence capture using PCR-generated probes: a cost-effective method of targeted high-throughput sequencing for nonmodel organisms.
Published: March, 2014

Abstract: Recent advances in high-throughput sequencing library preparation and subgenomic enrichment methods have opened new avenues for population genetics and phylogenetics of nonmodel organisms. To multiplex large numbers of indexed samples while sequen...
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mMAPS: a flow-proteometric technique to analyze protein-protein interactions in individual signaling complexes.
Published: March, 2014

Abstract: Signal transduction is a dynamic process that regulates cellular functions through multiple types of biomolecular interactions, such as the interactions between proteins and between proteins and nucleic acids. However, the techniques currently ava...
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Sequential adaptive introgression of the mitochondrial genome in Drosophila yakuba and Drosophila santomea.
Published: March, 2014

Abstract: Interspecific hybridization provides the unique opportunity for species to tap into genetic variation present in a closely related species and potentially take advantage of beneficial alleles. It has become increasingly clear that when hybridizati...
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Sequencing and assembly of the 22-gb loblolly pine genome.
Published: March, 2014

Abstract: Conifers are the predominant gymnosperm. The size and complexity of their genomes has presented formidable technical challenges for whole-genome shotgun sequencing and assembly. We employed novel strategies that allowed us to determine the lobloll...
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PGC7 suppresses TET3 for protecting DNA methylation.
Published: March, 2014

Abstract: Ten-eleven translocation (TET) family enzymes convert 5-methylcytosine to 5-hydroxylmethylcytosine. However, the molecular mechanism that regulates this biological process is not clear. Here, we show the evidence that PGC7 (also known as Dppa3 or ...
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The long non-coding RNA Paupar regulates the expression of both local and distal genes.
Published: February, 2014

Abstract: Although some long noncoding RNAs (lncRNAs) have been shown to regulate gene expression in cis, it remains unclear whether lncRNAs can directly regulate transcription in trans by interacting with chromatin genome-wide independently of their sites ...
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Long-term parental methamphetamine exposure of mice influences behavior and hippocampal DNA methylation of the offspring.
Published: February, 2014

Abstract: The high rate of methamphetamine (METH) abuse among young adults and women of childbearing age makes it imperative to determine the long-term effects of METH exposure on the offspring. We hypothesized that parental METH exposure modulates offsprin...
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C/EBPα poises B cells for rapid reprogramming into induced pluripotent stem cells.
Published: February, 2014

Abstract: CCAAT/enhancer binding protein-α (C/EBPα) induces transdifferentiation of B cells into macrophages at high efficiencies and enhances reprogramming into induced pluripotent stem (iPS) cells when co-expressed with the transcription factors Oct4 (Pou...
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Nonstochastic reprogramming from a privileged somatic cell state.
Published: February, 2014

Abstract: Reprogramming somatic cells to induced pluripotency by Yamanaka factors is usually slow and inefficient and is thought to be a stochastic process. We identified a privileged somatic cell state, from which acquisition of pluripotency could occur in...
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A deterministic analysis of genome integrity during neoplastic growth in Drosophila.
Published: February, 2014

Abstract: The development of cancer has been associated with the gradual acquisition of genetic alterations leading to a progressive increase in malignancy. In various cancer types this process is enabled and accelerated by genome instability. While genome ...
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Hundreds of circular novel plasmids and DNA elements identified in a rat cecum metamobilome.
Published: February, 2014

Abstract: Metagenomic approaches are widespread in microbiological research, but so far, the knowledge on extrachromosomal DNA diversity and composition has largely remained dependant on cultivating host organisms. Even with the emergence of metagenomics, c...
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Adult glucocorticoid exposure leads to transcriptional and DNA methylation changes in nuclear steroid receptors in the hippocampus and kidney of mouse male offspring.
Published: February, 2014

Abstract: Synthetic glucocorticoids (sGCs) are commonly prescribed for the management of inflammatory and endocrine disorders. However, nothing is known regarding the effects of sGC on adult germline methylome and whether these effects can be transmitted to...
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Assembly of the genome of the disease vector Aedes aegypti onto a genetic linkage map allows mapping of genes affecting disease transmission.
Published: January, 2014

Abstract: The mosquito Aedes aegypti transmits some of the most important human arboviruses, including dengue, yellow fever and chikungunya viruses. It has a large genome containing many repetitive sequences, which has resulted in the genome being poorly as...
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Peroxisome proliferator-activated receptor γ regulates genes involved in insulin/insulin-like growth factor signaling and lipid metabolism during adipogenesis through functionally distinct enhancer classes.
Published: January, 2014

Abstract: The nuclear receptor peroxisome proliferator-activated receptor (PPAR) is a transcription factor whose expression is induced during adipogenesis and that is required for the acquisition and control of mature adipocyte functions. Indeed, PPAR induc...
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Mutations in POGLUT1, encoding protein O-glucosyltransferase 1, cause autosomal-dominant Dowling-Degos disease.
Published: January, 2014

Abstract: Dowling-Degos disease (DDD) is an autosomal-dominant genodermatosis characterized by progressive and disfiguring reticulate hyperpigmentation. We previously identified loss-of-function mutations in KRT5 but were only able to detect pathogenic muta...
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The genome-wide landscape of DNA methylation and hydroxymethylation in response to sleep deprivation impacts on synaptic plasticity genes.
Published: January, 2014

Abstract: Sleep is critical for normal brain function and mental health. However, the molecular mechanisms mediating the impact of sleep loss on both cognition and the sleep electroencephalogram remain mostly unknown. Acute sleep loss impacts brain gene exp...
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Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants.
Published: January, 2014

Abstract: BACKGROUND: The source inoculum of gastrointestinal tract (GIT) microbes is largely influenced by delivery mode in full-term infants, but these influences may be decoupled in very low birth weight (VLBW,
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Differential methylation of the TRPA1 promoter in pain sensitivity.
Published: January, 2014

Abstract: Chronic pain is a global public health problem, but the underlying molecular mechanisms are not fully understood. Here we examine genome-wide DNA methylation, first in 50 identical twins discordant for heat pain sensitivity and then in 50 further ...
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Array-based assay detects genome-wide 5-mC and 5-hmC in the brains of humans, non-human primates, and mice.
Published: January, 2014

Abstract: BACKGROUND: Methylation on the fifth position of cytosine (5-mC) is an essential epigenetic mark that is linked to both normal neurodevelopment and neurological diseases. The recent identification of another modified form of cytosine, 5-hydroxymet...
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Viral aetiology influenza like illnesses in Santa Cruz, Bolivia (2010-2012).
Published: January, 2014

Abstract: BACKGROUND: Acute respiratory infections represent a serious public health issue worldwide but virological aetiologies of Influenza Like Illnesses (ILIs) remain largely unknown in developing countries. This study represents the first attempt to ch...
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Strand-specific RNA-Seq reveals widespread and developmentally regulated transcription of natural antisense transcripts in Plasmodium falciparum.
Published: January, 2014

Abstract: BACKGROUND: Advances in high-throughput sequencing have led to the discovery of widespread transcription of natural antisense transcripts (NATs) in a large number of organisms, where these transcripts have been shown to play important roles in the...
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Recessive mutations in a distal PTF1A enhancer cause isolated pancreatic agenesis.
Published: January, 2014

Abstract: The contribution of cis-regulatory mutations to human disease remains poorly understood. Whole-genome sequencing can identify all noncoding variants, yet the discrimination of causal regulatory mutations represents a formidable challenge. We used ...
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Genome-wide methylation and gene expression changes in newborn rats following maternal protein restriction and reversal by folic acid.
Published: December, 2013

Abstract: A large body of evidence from human and animal studies demonstrates that the maternal diet during pregnancy can programme physiological and metabolic functions in the developing fetus, effectively determining susceptibility to later disease. The m...
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The maize glossy13 gene, cloned via BSR-Seq and Seq-walking encodes a putative ABC transporter required for the normal accumulation of epicuticular waxes.
Published: December, 2013

Abstract: Aerial plant surfaces are covered by epicuticular waxes that among other purposes serve to control water loss. Maize glossy mutants originally identified by their "glossy" phenotypes exhibit alterations in the accumulation of epicuticular waxes. B...
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Transcription factor occupancy can mediate active turnover of DNA methylation at regulatory regions.
Published: December, 2013

Abstract: Distal regulatory elements, including enhancers, play a critical role in regulating gene activity. Transcription factor binding to these elements correlates with Low Methylated Regions (LMRs) in a process that is poorly understood. Here we ask whe...
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Rapid Transposon Liquid Enrichment Sequencing (TnLE-seq) for Gene Fitness Evaluation in Underdeveloped Bacterial Systems.
Published: December, 2013

Abstract: Whole-genome fitness analysis in microbes that uses saturating transposon mutagenesis combined with massively parallel sequencing (Tn-seq) is providing a measure of the contribution of each gene to a given growth condition. With this technique, ge...
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Alternative End-Joining and Classical Nonhomologous End-Joining Pathways Repair Different Types of Double-Strand Breaks during Class-Switch Recombination.
Published: December, 2013

Abstract: Classical nonhomologous end-joining (C-NHEJ) and alternative end-joining (A-EJ) are the main DNA double-strand break (DSB) repair pathways when a sister chromatid is not available. However, it is not clear how one pathway is chosen over the other ...
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Suggestive linkage of familial mesial temporal lobe epilepsy to chromosome 3q26.
Published: November, 2013

Abstract: PURPOSE: To describe the clinical findings in a family with a benign form of mesial temporal lobe epilepsy and to identify the causative genetic factors. METHODS: All participants were personally interviewed and underwent neurologic examination. T...
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Comparative analysis of affinity-based 5-hydroxymethylation enrichment techniques.
Published: November, 2013

Abstract: The epigenetic modification of 5-hydroxymethylcytosine (5hmC) is receiving great attention due to its potential role in DNA methylation reprogramming and as a cell state identifier. Given this interest, it is important to identify reliable and cos...
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High-resolution microbial community reconstruction by integrating short reads from multiple 16S rRNA regions.
Published: November, 2013

Abstract: The emergence of massively parallel sequencing technology has revolutionized microbial profiling, allowing the unprecedented comparison of microbial diversity across time and space in a wide range of host-associated and environmental ecosystems. A...
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Expression and regulation of intergenic long noncoding RNAs during T cell development and differentiation.
Published: November, 2013

Abstract: Although intergenic long noncoding RNAs (lincRNAs) have been linked to gene regulation in various tissues, little is known about lincRNA transcriptomes in the T cell lineages. Here we identified 1,524 lincRNA clusters in 42 T cell samples, from ea...
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The THO complex component Thp2 counteracts telomeric R-loops and telomere shortening.
Published: October, 2013

Abstract: Telomere maintenance by the conventional DNA replication machinery and telomerase is assisted by specialized DNA helicases, nucleases and telomere binding proteins. Here, we identify the THO components at telomeres and define critical roles of thi...
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Ligation bias in illumina next-generation DNA libraries: implications for sequencing ancient genomes.
Published: October, 2013

Abstract: Ancient DNA extracts consist of a mixture of endogenous molecules and contaminant DNA templates, often originating from environmental microbes. These two populations of templates exhibit different chemical characteristics, with the former showing ...
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Fine-Mapping an Association of FSHR with Preterm Birth in a Finnish Population.
Published: October, 2013

Abstract: Preterm birth is a complex disorder defined by gestations of less than 37 weeks. While preterm birth is estimated to have a significant genetic component, relative few genes have been associated with preterm birth. Polymorphism in one such gene, f...
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Diet Alters Both the Structure and Taxonomy of the Ovine Gut Microbial Ecosystem.
Published: October, 2013

Abstract: We surveyed the ruminal metagenomes of 16 sheep under two different diets using Illumina pair-end DNA sequencing of raw microbial DNA extracted from rumen samples. The resulting sequence data were bioinformatically mapped to known prokaryotic 16S ...
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Mu-seq: Sequence-Based Mapping and Identification of Transposon Induced Mutations.
Published: October, 2013

Abstract: Mutations tagged by transposon insertions can be readily mapped and identified in organisms with sequenced genomes. Collections of such mutants allow a systematic analysis of gene function, and can be sequence-indexed to build invaluable resources...
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Identification of genes expressed by immune cells of the colon that are regulated by colorectal cancer-associated variants.
Published: October, 2013

Abstract: A locus on human chromosome 11q23 tagged by marker rs3802842 was associated with colorectal cancer (CRC) in a genome-wide association study; this finding has been replicated in case-control studies worldwide. In order to identify biologic factors ...
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A missense mutation accelerating the gating of the lysosomal Cl-/H+-exchanger ClC-7/Ostm1 causes osteopetrosis with gingival hamartomas in cattle.
Published: October, 2013

Abstract: Chloride/proton exchange by the lysosomal anion transporter ClC-7/Ostm1 is of pivotal importance for the physiology of lysosomes and bone resorption. Mice lacking either ClC-7 or Ostm1 develop a lysosomal storage disease and mutations in either pr...
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Evidence of population bottleneck in Astragalus michauxii (Fabaceae), a narrow endemic of the southeastern United States
Published: October, 2013

Abstract: Genetic factors such as decreased genetic diversity and increased homozygosity can have detrimental effects on rare species, and may ultimately limit potential adaptation and exacerbate population declines. The Gulf and Atlantic Coastal Plain phys...
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Global DNA methylation screening of liver in piperonyl butoxide-treated mice in a two-stage hepatocarcinogenesis model.
Published: October, 2013

Abstract: Disruptive epigenetic gene control has been shown to be involved in carcinogenesis. To identify key molecules in piperonyl butoxide (PBO)-induced hepatocarcinogenesis, we searched hypermethylated genes using CpG island (CGI) microarrays in non-neo...
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Whole-exome sequencing supports genetic heterogeneity in childhood apraxia of speech.
Published: October, 2013

Abstract: The genetic basis of complex neurological disorders involving language are poorly understood, partly due to the multiple additive genetic risk factors that are thought to be responsible. Furthermore, these conditions are often syndromic in that th...
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Oxidative bisulfite sequencing of 5-methylcytosine and 5-hydroxymethylcytosine.
Published: October, 2013

Abstract: To uncover the function of and interplay between the mammalian cytosine modifications 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC), new techniques and advances in current technology are needed. To this end, we have developed oxidative...
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Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues.
Published: October, 2013

Abstract: Mammalian development requires cytosine methylation, a heritable epigenetic mark of cellular memory believed to maintain a cell's unique gene expression pattern. However, it remains unclear how dynamic DNA methylation relates to cell type-specific...
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Genome-Wide Analysis of DNA Methylation in Soybean.
Published: September, 2013

Abstract: Cytosine methylation is an important mechanism for dynamical regulation of gene expression. We identified 2162 differentially methylated regions in different soybean organs and further analyzed the interplays among DNA methylation, smRNA abundance...
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The BTB-Containing Protein Kctd15 Is SUMOylated In Vivo.
Published: September, 2013

Abstract: Potassium Channel Tetramerization Domain containing 15 (Kctd15) has a role in regulating the neural crest (NC) domain in the embryo. Kctd15 inhibits NC induction by antagonizing Wnt signaling and by interaction with the transcription factor AP-2α ...
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Human telomeres that carry an integrated copy of human herpesvirus 6 are often short and unstable, facilitating release of the viral genome from the chromosome.
Published: September, 2013

Abstract: Linear chromosomes are stabilized by telomeres, but the presence of short dysfunctional telomeres triggers cellular senescence in human somatic tissues, thus contributing to ageing. Approximately 1% of the population inherits a chromosomally integ...
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Recent Diversification of a Marine Genus (Tursiops spp.) Tracks Habitat Preference and Environmental Change.
Published: September, 2013

Abstract: Understanding the evolution of diversity and the resulting systematics in marine systems is confounded by the lack of clear boundaries in oceanic habitats, especially for highly mobile species like marine mammals. Dolphin populations and sibling s...
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Exome sequencing identifies recurring FLT3 N676K mutations in core-binding factor leukemia.
Published: September, 2013

Abstract: The t(8;21) and inv(16)/t(16;16) rearrangements affecting the core-binding factors RUNX1 and CBFB, respectively, are found in 15% to 20% of adult de novo acute myeloid leukemia (AML) cases and are associated with a favorable prognosis. Since the e...
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Insights into the Loblolly Pine Genome: Characterization of BAC and Fosmid Sequences.
Published: September, 2013

Abstract: Despite their prevalence and importance, the genome sequences of loblolly pine, Norway spruce, and white spruce, three ecologically and economically important conifer species, are just becoming available to the research community. Following the co...
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Global alterations of DNA methylation in cholangiocarcinoma targets the Wnt signaling pathway
Published: September, 2013

Abstract: The molecular mechanisms underlying the genesis of cholangiocarcinomas (CCs) are poorly understood. Epigenetic changes such as aberrant hypermethylation and subsequent atypical gene expression are characteristic features of most human cancers. In ...
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Antisense transcripts enhanced by camptothecin at divergent CpG-island promoters associated with bursts of topoisomerase I-DNA cleavage complex and R-loop formation.
Published: September, 2013

Abstract: DNA Topoisomerase I (Top1) is required to relax DNA supercoils generated by RNA polymerases (RNAPs). Top1 is inhibited with high specificity by camptothecin (CPT), an effective anticancer agent, and by oxidative base damage and ribonucleotides in ...
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Integrated virus-host methylome analysis in head and neck squamous cell carcinoma
Published: September, 2013

Abstract: One in six cancers worldwide is caused by infection and human papillomavirus (HPV) is one of the main culprits. To better understand the dynamics of HPV integration and its effect on both the viral and host methylomes, we conducted whole-genome DN...
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Unisexual and heterosexual meiotic reproduction generate aneuploidy and phenotypic diversity de novo in the yeast Cryptococcus neoformans.
Published: September, 2013

Abstract: Aneuploidy is known to be deleterious and underlies several common human diseases, including cancer and genetic disorders such as trisomy 21 in Down's syndrome. In contrast, aneuploidy can also be advantageous and in fungi confers antifungal drug ...
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A metagenomic snapshot of taxonomic and functional diversity in an alpine glacier cryoconite ecosystem
Published: September, 2013

Abstract: Cryoconite is a microbe–mineral aggregate which darkens the ice surface of glaciers. Microbial process and marker gene PCR-dependent measurements reveal active and diverse cryoconite microbial communities on polar glaciers. Here, we provide the fi...
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Epigenetic silencing of Bim transcription by Spi-1/PU.1 promotes apoptosis resistance in leukaemia.
Published: September, 2013

Abstract: Deregulation of transcriptional networks contributes to haematopoietic malignancies. The transcription factor Spi-1/PU.1 is a master regulator of haematopoiesis and its alteration leads to leukaemia. Spi-1 overexpression inhibits differentiation a...
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Mass production of SNP markers in a nonmodel passerine bird through RAD sequencing and contig mapping to the zebra finch genome.
Published: September, 2013

Abstract: Here, we present an adaptation of restriction-site-associated DNA sequencing (RAD-seq) to the Illumina HiSeq2000 technology that we used to produce SNP markers in very large quantities at low cost per unit in the Réunion grey white-eye (Zosterops ...
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Vitamin C induces Tet-dependent DNA demethylation and a blastocyst-like state in ES cells.
Published: August, 2013

Abstract: DNA methylation is a heritable epigenetic modification involved in gene silencing, imprinting, and the suppression of retrotransposons. Global DNA demethylation occurs in the early embryo and the germ line, and may be mediated by Tet (ten eleven t...
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Mitochondrial genome linearization is a causative factor for cardiomyopathy in mice and Drosophila.
Published: August, 2013

Abstract: Aims: Mitofusin (Mfn) 2 redundantly promotes mitochondrial outer membrane tethering and organelle fusion with Mfn1, and uniquely functions as the mitochondrial receptor for Parkin during PINK1-Parkin mediated mitophagy. Selective deletion of Mfn2 ...
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High-throughput sequencing reveals principles of adeno-associated virus serotype 2 integration.
Published: August, 2013

Abstract: Viral integrations are important in human biology, yet genome-wide integration profiles have not been determined for many viruses. Adeno-associated virus (AAV) infects most of the human population and is a prevalent gene therapy vector. AAV integr...
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Minotaur is critical for primary piRNA biogenesis.
Published: August, 2013

Abstract: Piwi proteins and their associated small RNAs are essential for fertility in animals. In part, this is due to their roles in guarding germ cell genomes against the activity of mobile genetic elements. piRNA populations direct Piwi proteins to sile...
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Chromatin-modifying agents reactivate embryonic renal stem/progenitor genes in human adult kidney epithelial cells but abrogate dedifferentiation and stemness.
Published: August, 2013

Abstract: Abstract Recent studies have suggested that epigenetic modulation with chromatin-modifying agents can induce stemness and dedifferentiation and increase developmental plasticity. For instance, valproic acid (VPA), a histone deacetylase (HDAC) inhi...
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DNA unmethylome profiling by covalent capture of CpG sites.
Published: July, 2013

Abstract: Dynamic patterns of cytosine-5 methylation and successive hydroxylation are part of epigenetic regulation in eukaryotes, including humans, which contributes to normal phenotypic variation and disease risk. Here we present an approach for the mappi...
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DNA methylation of dermal MSCs in psoriasis: Identification of epigenetically dysregulated genes.
Published: July, 2013

Abstract: BACKGROUND: Mesenchymal stem cells (MSCs) are likely involved in pathological processes of immune-related diseases, including psoriasis, because of their immunoregulatory and pro-angiogenic effects. DNA methylation plays an essential role in regul...
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An epigenetic trap stabilizes singular olfactory receptor expression.
Published: July, 2013

Abstract: The molecular mechanisms regulating olfactory receptor (OR) expression in the mammalian nose are not yet understood. Here, we identify the transient expression of histone demethylase LSD1 and the OR-dependent expression of adenylyl cyclase 3 (Adcy...
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Transcriptional profiling by RNA-Seq of peri-attachment porcine embryos generated by a variety of assisted reproductive technologies.
Published: July, 2013

Abstract: Substantial mortality of in vitro manipulated porcine embryos is observed during peri-attachment development. Herein we describe our efforts to characterize the transcriptomes of embryonic disc (ED) and trophectoderm (TE) cells from porcine embryo...
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De Novo DNA Methylation in the Male Germ Line Occurs by Default but Is Excluded at Sites of H3K4 Methylation.
Published: July, 2013

Abstract: To understand what dictates the emerging patterns of de novo DNA methylation in the male germline, we mapped DNA methylation, chromatin, and transcription changes in purified fetal mouse germ cells by using methylated CpG island recovery assay (MI...
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Digital genotyping of sorghum -- a diverse plant species with a large repeat-rich genome.
Published: July, 2013

Abstract: BACKGROUND: Rapid acquisition of accurate genotyping information is essential for all genetic marker-based studies. For species with relatively small genomes, complete genome resequencing is a feasible approach for genotyping; however, for species...
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Improved genetic testing for monogenic diabetes using targeted next-generation sequencing.
Published: June, 2013

Abstract: AIMS/HYPOTHESIS: Current genetic tests for diagnosing monogenic diabetes rely on selection of the appropriate gene for analysis according to the patient's phenotype. Next-generation sequencing enables the simultaneous analysis of multiple genes in...
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Senescence-associated lncRNAs: senescence-associated long noncoding RNAs.
Published: June, 2013

Abstract: Noncoding RNAs include small transcripts, such as microRNAs and piwi-interacting RNAs, and a wide range of long noncoding RNAs (lncRNAs). Although many lncRNAs have been identified, only a small number of lncRNAs have been characterized functional...
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Discovery of potential new gene variants and inflammatory cytokine associations with fibromyalgia syndrome by whole exome sequencing.
Published: June, 2013

Abstract: Fibromyalgia syndrome (FMS) is a chronic musculoskeletal pain disorder affecting 2% to 5% of the general population. Both genetic and environmental factors may be involved. To ascertain in an unbiased manner which genes play a role in the disorder...
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HPV-related methylation signature predicts survival in oropharyngeal squamous cell carcinomas.
Published: June, 2013

Abstract: High-risk types of human papilloma virus (HPV) are increasingly associated with oropharyngeal squamous cell carcinoma (OPSCC). Strikingly, patients with HPV-positive OPSCC are highly curable with ionizing radiation and have better survival compare...
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Reference-free SNP discovery for the Eurasian beaver from restriction site-associated DNA paired-end data.
Published: June, 2013

Abstract: In this study, we used restriction site-associated DNA (RAD) sequencing to discover SNP markers suitable for population genetic and parentage analysis with the aim of using them for monitoring the reintroduction of the Eurasian beaver (Castor fibr...
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Dynamic changes in 5-hydroxymethylation signatures underpin early and late events in drug exposed liver.
Published: June, 2013

Abstract: Aberrant DNA methylation is a common feature of neoplastic lesions, and early detection of such changes may provide powerful mechanistic insights and biomarkers for carcinogenesis. Here, we investigate dynamic changes in the mouse liver DNA methyl...
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Characterization of the DNA methylome and its interindividual variation in human peripheral blood monocytes.
Published: June, 2013

Abstract: AIM: Peripheral blood monocytes (PBMs) play multiple and critical roles in the immune response, and abnormalities in PBMs have been linked to a variety of human disorders. However, the DNA methylation landscape in PBMs is largely unknown. In this ...
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Global regulation of promoter melting in naive lymphocytes.
Published: May, 2013

Abstract: Lymphocyte activation is initiated by a global increase in messenger RNA synthesis. However, the mechanisms driving transcriptome amplification during the immune response are unknown. By monitoring single-stranded DNA genome wide, we show that the...
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Region of difference 4 in alpine Mycobacterium caprae isolates indicates three variants.
Published: May, 2013

Abstract: The lack of complete genome sequence information for Mycobacterium caprae complicates a robust differentiation of M. caprae and Mycobacterium bovis. In this study, the presence or absence of M. caprae-specific single nucleotide polymorphisms in le...
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Sulforaphane enhances Nrf2 expression in prostate cancer TRAMP C1 cells through epigenetic regulation.
Published: May, 2013

Abstract: Growing evidence suggests epigenetic alteration is involved during the development and progression of prostate cancer. Previously, we found Nrf2, a key regulator of cellular antioxidant defense systems, was silenced through epigenetic mechanism du...
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G-quadruplex structures are stable and detectable in human genomic DNA.
Published: April, 2013

Abstract: The G-quadruplex is an alternative DNA structural motif that is considered to be functionally important in the mammalian genome for transcriptional regulation, DNA replication and genome stability, but the nature and distribution of G-quadruplexes...
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Genome-wide analysis reveals TET- and TDG-dependent 5-methylcytosine oxidation dynamics.
Published: April, 2013

Abstract: TET dioxygenases successively oxidize 5-methylcytosine (5mC) in mammalian genomes to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). 5fC/5caC can be excised and repaired to regenerate unmodified cytosines by ...
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The developmental epigenomics toolbox: ChIP-seq and MethylCap-seq profiling of early zebrafish embryos.
Published: April, 2013

Abstract: Genome-wide profiling of DNA methylation and histone modifications answered many questions as to how the genes are regulated on a global scale and what their epigenetic makeup is. Yet, little is known about the function of these marks during early...
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Association between living environment and human oral viral ecology.
Published: April, 2013

Abstract: The human oral cavity has an indigenous microbiota known to include a robust community of viruses. Very little is known about how oral viruses are spread throughout the environment or to which viruses individuals are exposed. We sought to determin...
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A Culture-Independent Sequence-Based Metage nomics Approach to the Investigation of an Outbreak of Shiga-Toxigenic Escherichia coli O104:H4
Published: April, 2013

Abstract: Importance Identification of the bacterium responsible for an outbreak can aid in disease management. However, traditional culture-based diagnosis can be difficult, particularly if no specific diagnostic test is available for an outbreak strain...
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Genome-wide comparison of DNA hydroxymethylation in mouse embryonic stem cells and neural progenitor cells by a new comparative hMeDIP-seq method.
Published: April, 2013

Abstract: The genome-wide distribution patterns of the '6th base' 5-hydroxymethylcytosine (5hmC) in many tissues and cells have recently been revealed by hydroxymethylated DNA immunoprecipitation (hMeDIP) followed by high throughput sequencing or tiling arr...
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Duration of fecal shedding of Shiga toxin-producing Escherichia coli O104:H4 in patients infected during the 2011 outbreak in Germany: a multicenter study.
Published: April, 2013

Abstract: BACKGROUND: In May-July 2011, Germany experienced a large food-borne outbreak of Shiga toxin 2-producing Escherichia coli (STEC O104:H4) with 3842 cases, including 855 cases with hemolytic uremic syndrome (HUS) and 53 deaths. METHODS: A multicente...
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De novo sequencing of hazelnut bacterial artificial chromosomes (BACs) using multiplex Illumina sequencing and targeted marker development for eastern filbert blight resistance
Published: April, 2013

Abstract: Bacterial artificial chromosome (BAC) libraries are widely used in map-based cloning of plant genes. Eastern filbert blight (EFB), caused by the pyrenomycete Anisogramma anomala (Peck) E. Müller, is a devastating disease of European hazelnut (Cory...
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Epigenetic upregulation of lncRNAs at 13q14.3 in leukemia is linked to the In Cis downregulation of a gene cluster that targets NF-kB.
Published: April, 2013

Abstract: Non-coding RNAs are much more common than previously thought. However, for the vast majority of non-coding RNAs, the cellular function remains enigmatic. The two long non-coding RNA (lncRNA) genes DLEU1 and DLEU2 map to a critical region at chromo...
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Genomic evidence for island population conversion resolves conflicting theories of polar bear evolution.
Published: March, 2013

Abstract: Despite extensive genetic analysis, the evolutionary relationship between polar bears (Ursus maritimus) and brown bears (U. arctos) remains unclear. The two most recent comprehensive reports indicate a recent divergence with little subsequent admi...
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H2-independent growth of the hydrogenotrophic methanogen Methanococcus maripaludis.
Published: February, 2013

Abstract: UNLABELLED: Hydrogenotrophic methanogenic Archaea require reduced ferredoxin as an anaplerotic source of electrons for methanogenesis. H(2) oxidation by the hydrogenase Eha provides these electrons, consistent with an H(2) requirement for growth. ...
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Mitochondrial phylogenomics of modern and ancient equids.
Published: February, 2013

Abstract: The genus Equus is richly represented in the fossil record, yet our understanding of taxonomic relationships within this genus remains limited. To estimate the phylogenetic relationships among modern horses, zebras, asses and donkeys, we generated...
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DNA methylation analysis in the intestinal epithelium-effect of cell separation on gene expression and methylation profile.
Published: February, 2013

Abstract: BACKGROUND: Epigenetic signatures are highly cell type specific. Separation of distinct cell populations is therefore desirable for all epigenetic studies. However, to date little information is available on whether separation protocols might infl...
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Consequences of normalizing transcriptomic and genomic libraries of plant genomes using a duplex-specific nuclease and tetramethylammonium chloride.
Published: February, 2013

Abstract: Several applications of high throughput genome and transcriptome sequencing would benefit from a reduction of the high-copy-number sequences in the libraries being sequenced and analyzed, particularly when applied to species with large genomes. We...
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DNA methylation mediated control of gene expression is critical for development of crown gall tumors.
Published: February, 2013

Abstract: Crown gall tumors develop after integration of the T-DNA of virulent Agrobacterium tumefaciens strains into the plant genome. Expression of the T-DNA-encoded oncogenes triggers proliferation and differentiation of transformed plant cells. Crown ga...
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Evolutionary potential, cross-stress behavior and the genetic basis of acquired stress resistance in Escherichia coli.
Published: February, 2013

Abstract: Bacterial populations have a remarkable capacity to cope with extreme environmental fluctuations in their natural environments. In certain cases, adaptation to one stressful environment provides a fitness advantage when cells are exposed to a seco...
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LBR and Lamin A/C Sequentially Tether Peripheral Heterochromatin and Inversely Regulate Differentiation.
Published: January, 2013

Abstract: Eukaryotic cells have a layer of heterochromatin at the nuclear periphery. To investigate mechanisms regulating chromatin distribution, we analyzed heterochromatin organization in different tissues and species, including mice with mutations in the...
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Targeted multiplex next-generation sequencing: advances in techniques of mitochondrial and nuclear DNA sequencing for population genomics.
Published: January, 2013

Abstract: Next-generation sequencing (NGS) is emerging as an efficient and cost-effective tool in population genomic analyses of nonmodel organisms, allowing simultaneous resequencing of many regions of multi-genomic DNA from multiplexed samples. Here, we d...
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The Roles of Whole-Genome and Small-Scale Duplications in the Functional Specialization of Saccharomyces cerevisiae Genes.
Published: January, 2013

Abstract: Researchers have long been enthralled with the idea that gene duplication can generate novel functions, crediting this process with great evolutionary importance. Empirical data shows that whole-genome duplications (WGDs) are more likely to be ret...
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Identification of differentially methylated regions using streptavidin bisulfite ligand methylation enrichment (SuBLiME), a new method to enrich for methylated DNA prior to deep bisulfite genomic sequencing
Published: January, 2013

Abstract: We have developed a method that enriches for methylated cytosines by capturing the fraction of bisulfite-treated DNA with unconverted cytosines. The method, called streptavidin bisulfite ligand methylation enrichment (SuBLiME), involves the specif...
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53BP1 Alters the Landscape of DNA Rearrangements and Suppresses AID-Induced B Cell Lymphoma.
Published: January, 2013

Abstract: Deficiencies in factors that regulate the DNA damage response enhance the incidence of malignancy by destabilizing the genome. However, the precise influence of the DNA damage response on regulation of cancer-associated rearrangements is not well ...
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Identification of Novel Imidazo[1,2-a]pyridine Inhibitors Targeting M. tuberculosis QcrB.
Published: December, 2012

Abstract: Mycobacterium tuberculosis is a major human pathogen and the causative agent for the pulmonary disease, tuberculosis (TB). Current treatment programs to combat TB are under threat due to the emergence of multi-drug and extensively-drug resistant T...
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Evolution of cichlid vision via trans-regulatory divergence.
Published: December, 2012

Abstract: ABSTRACT: BACKGROUND: Phenotypic evolution may occur through mutations that affect either the structure or expression of protein-coding genes. Although the evolution of color vision has historically been attributed to structural mutations within t...
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Structural analysis of the genome of breast cancer cell line ZR-75-30 identifies twelve expressed fusion genes.
Published: December, 2012

Abstract: ABSTRACT: BACKGROUND: It has recently emerged that common epithelial cancers such as breast cancers have fusion genes like those in leukaemias. In a representative breast cancer cell line, ZR-75-30, we searched for fusion genes, by analysing genom...
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Next-Generation Sequencing Reveals Deep Intronic Cryptic ABCC8 and HADH Splicing Founder Mutations Causing Hyperinsulinism by Pseudoexon Activation.
Published: December, 2012

Abstract: Next-generation sequencing (NGS) enables analysis of the human genome on a scale previously unachievable by Sanger sequencing. Exome sequencing of the coding regions and conserved splice sites has been very successful in the identification of dise...
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A polycomb group protein is retained at specific sites on chromatin in mitosis.
Published: December, 2012

Abstract: Epigenetic regulation of gene expression, including by Polycomb Group (PcG) proteins, may depend on heritable chromatin states, but how these states can be propagated through mitosis is unclear. Using immunofluorescence and biochemical fractionati...
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Nano-MeDIP-seq: Methylome analysis using low DNA concentrations (Prot 58)
Published: December, 2012

Abstract: To understand the functional consequences of DNA methylation on phenotypic plasticity, a genome - wide analysis should be embraced. This in turn requires a technique that balances accuracy, genome coverage, resolution and cost, yet is low in DNA i...
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TET2 promotes histone O-GlcNAcylation during gene transcription.
Published: December, 2012

Abstract: Ten eleven translocation (TET) enzymes, including TET1, TET2 and TET3, convert 5-methylcytosine to 5-hydroxymethylcytosine and regulate gene transcription. However, the molecular mechanism by which TET family enzymes regulate gene transcription re...
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Recurrent targeted genes of hepatitis B virus in the liver cancer genomes identified by a next-generation sequencing-based approach.
Published: December, 2012

Abstract: Integration of the viral DNA into host chromosomes was found in most of the hepatitis B virus (HBV)-related hepatocellular carcinomas (HCCs). Here we devised a massive anchored parallel sequencing (MAPS) method using next-generation sequencing to ...
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Population genomics of Pacific lamprey: adaptive variation in a highly dispersive species.
Published: December, 2012

Abstract: Unlike most anadromous fishes that have evolved strict homing behaviour, Pacific lamprey (Entosphenus tridentatus) seem to lack philopatry as evidenced by minimal population structure across the species range. Yet unexplained findings of within-re...
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Mechanistic and structural insight into the functional dichotomy between IL-2 and IL-15.
Published: December, 2012

Abstract: Interleukin 15 (IL-15) and IL-2 have distinct immunological functions even though both signal through the receptor subunit IL-2Rβ and the common γ-chain (γ(c)). Here we found that in the structure of the IL-15-IL-15Rα-IL-2Rβ-γ(c) quaternary comple...
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Genome Sequence of OXA-48 Carbapenemase-Producing Klebsiella pneumoniae KpO3210.
Published: December, 2012

Abstract: Klebsiella pneumoniae KpO3210 is a OXA-48 carbapenemase-producing isolate obtained from a blood culture in the context of an outbreak in Hospital Universitario La Paz (Madrid, Spain) in 2010. It belongs to the major clone detected during the outbr...
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Molecular characterization of transgene integration by next-generation sequencing in transgenic cattle.
Published: November, 2012

Abstract: As the number of transgenic livestock increases, reliable detection and molecular characterization of transgene integration sites and copy number are crucial not only for interpreting the relationship between the integration site and the specific ...
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Two different high throughput sequencing approaches identify thousands of de novo genomic markers for the genetically depleted bornean elephant.
Published: November, 2012

Abstract: High throughput sequencing technologies are being applied to an increasing number of model species with a high-quality reference genome. The application and analyses of whole-genome sequence data in non-model species with no prior genomic informat...
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Capturing native long-range contiguity by in situ library construction and optical sequencing.
Published: November, 2012

Abstract: The relatively short read lengths associated with the most cost-effective DNA sequencing technologies have limited their use in de novo genome assembly, structural variation detection, and haplotype-resolved genome sequencing. Consequently, there ...
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Timing of Transcriptional Quiescence during Gametogenesis Is Controlled by Global Histone H3K4 Demethylation.
Published: November, 2012

Abstract: Gametes are among the most highly specialized cells produced during development. Although gametogenesis culminates in transcriptional quiescence in plants and animals, regulatory mechanisms controlling this are unknown. Here, we confirm that gamet...
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A Forward Genetic Screen Identifies Eukaryotic Translation Initiation Factor 3, Subunit H (eIF3h), as an Enhancer of Variegation in the Mouse.
Published: November, 2012

Abstract: We have used a forward genetic screen to identify genes required for transgene silencing in the mouse. Previously these genes were found using candidate-based sequencing, a slow and labor-intensive process. Recently, whole-exome deep sequencing ha...
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CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters.
Published: October, 2012

Abstract: One clear hallmark of mammalian promoters is the presence of CpG islands (CGIs) at more than two-thirds of genes, whereas TATA boxes are only present at a minority of promoters. Using genome-wide approaches, we show that GC content and CGIs are ma...
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MeDIP coupled with a promoter tiling array as a platform to investigate global DNA methylation patterns in AML cells.
Published: October, 2012

Abstract: Hypermethylation of CpGs in promoter regions and subsequent changes in gene expression are common features in acute myeloid leukemia (AML). Genome-wide studies of the methylome are not only useful to understand changes in DNA methylation and gene ...
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The Many Landscapes of Recombination in Drosophila melanogaster.
Published: October, 2012

Abstract: Recombination is a fundamental biological process with profound evolutionary implications. Theory predicts that recombination increases the effectiveness of selection in natural populations. Yet, direct tests of this prediction have been restricte...
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Oxidative stress-regulated lentiviral TK/GCV gene therapy for lung cancer treatment.
Published: October, 2012

Abstract: NRF2 is a transcription factor that regulates protection against a wide variety of toxic insults to cells, including cytotoxic cancer chemotherapeutic drugs. Many lung cancer cells harbor a mutation in either NRF2 or its inhibitor KEAP1 resulting ...
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Initial Characterization of the Pf-Int Recombinase from the Malaria Parasite Plasmodium falciparum.
Published: October, 2012

Abstract: BACKGROUND: Genetic variation is an essential means of evolution and adaptation in many organisms in response to environmental change. Certain DNA alterations can be carried out by site-specific recombinases (SSRs) that fall into two families: the...
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Read length versus Depth of Coverage for Viral Quasispecies Reconstruction.
Published: October, 2012

Abstract: Recent advancements of sequencing technology have opened up unprecedented opportunities in many application areas. Virus samples can now be sequenced efficiently with very deep coverage to infer the genetic diversity of the underlying virus popula...
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Non-genotoxic carcinogen exposure induces defined changes in the 5-hydroxymethylome.
Published: October, 2012

Abstract: ABSTRACT: BACKGROUND: Induction and promotion of liver cancer by exposure to non-genotoxic carcinogens coincides with epigenetic perturbations, including specific changes in DNA methylation. Here we investigate the genome-wide dynamics of 5-hydro...
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Features of the Arabidopsis recombination landscape resulting from the combined loss of sequence variation and DNA methylation.
Published: October, 2012

Abstract: The rate of meiotic crossing over (CO) varies considerably along chromosomes, leading to marked distortions between physical and genetic distances. The causes underlying this variation are being unraveled, and DNA sequence and chromatin states hav...
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The GLIB technique for genome-wide mapping of 5-hydroxymethylcytosine.
Published: October, 2012

Abstract: 5-Hydroxymethylcytosine (5hmC) is a newly discovered DNA base present at detectable levels in most mammalian cell types and tissues. It is generated by Tet-enzyme-mediated oxidation of 5-methylcytosine (5mC). 5hmC is important both because of its ...
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Promoter DNA methylation couples genome-defence mechanisms to epigenetic reprogramming in the mouse germline.
Published: October, 2012

Abstract: Mouse primordial germ cells (PGCs) erase global DNA methylation (5mC) as part of the comprehensive epigenetic reprogramming that occurs during PGC development. 5mC plays an important role in maintaining stable gene silencing and repression of tran...
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Draft Genome Sequence of Lactobacillus rossiae DSM 15814T.
Published: October, 2012

Abstract: The draft genome sequence of Lactobacillus rossiae DSM 15814(T) (CS1, ATCC BAA-88) was determined by a whole-genome shotgun approach. Reads were assembled to a 2.9-Mb draft version. RAST genome annotation evidenced 2,723 predicted coding sequences...
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Human-specific CpG "beacons" identify loci associated with human-specific traits and disease.
Published: October, 2012

Abstract: Regulatory change has long been hypothesized to drive the delineation of the human phenotype from other closely related primates. Here we provide evidence that CpG dinucleotides play a special role in this process. CpGs enable epigenome variabilit...
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TET1 Suppresses Cancer Invasion by Activating the Tissue Inhibitors of Metalloproteinases.
Published: September, 2012

Abstract: Tumor suppressor gene silencing through cytosine methylation contributes to cancer formation. Whether DNA demethylation enzymes counteract this oncogenic effect is unknown. Here, we show that TET1, a dioxygenase involved in cytosine demethylation,...
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Tet2 Facilitates the Derepression of Myeloid Target Genes during CEBPα-Induced Transdifferentiation of Pre-B Cells.
Published: September, 2012

Abstract: The methylcytosine hydroxylase Tet2 has been implicated in hematopoietic differentiation and the formation of myeloid malignancies when mutated. An ideal system to study the role of Tet2 in myelopoeisis is CEBPα-induced transdifferentiation of pre...
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A mechanistic basis for amplification differences between samples and between genome regions.
Published: September, 2012

Abstract: ABSTRACT: BACKGROUND: For many analytical methods the efficiency of DNA amplification varies across the genome and between samples. The most affected genome regions tend to correlate with high C + G content, however this relationship is complex an...
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BZLF1 Governs CpG-Methylated Chromatin of Epstein-Barr Virus Reversing Epigenetic Repression.
Published: September, 2012

Abstract: Epigenetic mechanisms are essential for the regulation of all genes in mammalian cells but transcriptional repression including DNA methylation are also major epigenetic mechanisms of defense inactivating potentially harmful pathogens. Epstein-Bar...
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Genome-wide distribution of 5-formylcytosine in ES cells is associated with transcription and depends on thymine DNA glycosylase.
Published: August, 2012

Abstract: ABSTRACT: BACKGROUND: Methylation of cytosine in DNA (5mC) is an important epigenetic mark that is involved in the regulation of genome function. During early embryonic development in mammals, the methylation landscape is dynamically reprogrammed ...
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Characterization of eight polymorphic loci for Maasai giraffe (Giraffa camelopardalis tippelskirchi) using non-invasive genetic samples
Published: August, 2012

Abstract: We used Illumina sequencing to develop eight novel microsatellite loci for Maasai giraffe (Giraffa camelopardalis tippelskirchi), and screened them using fecal DNA. Genetic diversity was assessed for 40 individuals from the Katavi National Park/Ru...
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Mutations in isocitrate dehydrogenase 1 and 2 occur frequently in intrahepatic cholangiocarcinomas and share hypermethylation targets with glioblastomas.
Published: July, 2012

Abstract: Mutations in the genes encoding isocitrate dehydrogenase, IDH1 and IDH2, have been reported in gliomas, myeloid leukemias, chondrosarcomas and thyroid cancer. We discovered IDH1 and IDH2 mutations in 34 of 326 (10%) intrahepatic cholangiocarcinoma...
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SATB1-mediated Functional Packaging of Chromatin into Loops.
Published: July, 2012

Abstract: Mammalian genomes are organized into multiple layers of higher-order chromatin structure, and in this organization chromatin looping is a striking and crucial feature that brings together distal genomic loci into close spatial proximity. Such thre...
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An investigation of the affinities, specificity and kinetics involved in the interaction between the Yin Yang 1 transcription factor and DNA.
Published: July, 2012

Abstract: Human transcription factor Yin Yang 1 (YY1) is a four-zinc-finger protein that regulates a large number of genes with different biological functions in processes such as development, carcinogenesis and B-cell maturation. The natural binding sites ...
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Separating the wheat from the chaff: mitigating the effects of noise in a plastome phylogenomic data set from Pinus L. (Pinaceae).
Published: June, 2012

Abstract: ABSTRACT: BACKGROUND: Through next-generation sequencing, the amount of sequence data potentially available for phylogenetic analyses has increased exponentially in recent years. Simultaneously, the risk of incorporating 'noisy' data with misleadi...
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Fluorescence-based phenotypic selection allows forward genetic screens in haploid human cells.
Published: June, 2012

Abstract: The isolation of haploid cell lines has recently allowed the power of forward genetic screens to be applied to mammalian cells. The interest in applying this powerful genetic approach to a mammalian system is only tempered by the limited utility o...
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Bovine polledness - an autosomal dominant trait with allelic heterogeneity.
Published: June, 2012

Abstract: The persistent horns are an important trait of speciation for the family Bovidae with complex morphogenesis taking place briefly after birth. The polledness is highly favourable in modern cattle breeding systems but serious animal welfare issues u...
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Targeted re-sequencing of the allohexaploid wheat exome.
Published: June, 2012

Abstract: Bread wheat, Triticum aestivum, is an allohexaploid composed of the three distinct ancestral genomes, A, B and D. The polyploid nature of the wheat genome together with its large size has limited our ability to generate the significant amount of s...
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Rsx is a metatherian RNA with Xist-like properties in X-chromosome inactivation.
Published: June, 2012

Abstract: In female (XX) mammals, one of the two X chromosomes is inactivated to ensure an equal dose of X-linked genes with males (XY). X-chromosome inactivation in eutherian mammals is mediated by the non-coding RNA Xist. Xist is not found in metatherians...
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Whole-Exome Sequencing and High Throughput Genotyping Identified KCNJ11 as the Thirteenth MODY Gene.
Published: June, 2012

Abstract: BACKGROUND: Maturity-onset of the young (MODY) is a clinically heterogeneous form of diabetes characterized by an autosomal-dominant mode of inheritance, an onset before the age of 25 years, and a primary defect in the pancreatic beta-cell functio...
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Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription.
Published: June, 2012

Abstract: DNA cytosine methylation regulates gene expression in mammals. In bacteria, its role in gene expression and genome architecture is less understood. Here we perform high-throughput sequencing of bisulfite-treated genomic DNA from Escherichia coli K...
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Disruptive cell cycle regulation involving epigenetic downregulation of Cdkn2a (p16(Ink4a)) in early-stage liver tumor-promotion facilitating liver cell regeneration in rats.
Published: May, 2012

Abstract: Cell cycle aberration was immunohistochemically examined in relation to preneoplastic liver cell foci expressing glutathione S-transferase placental form (GST-P) at early stages of tumor-promotion in rats with thioacetamide (TAA), a hepatocarcinog...
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Evolution of Burkholderia pseudomallei in Recurrent Melioidosis.
Published: May, 2012

Abstract: Burkholderia pseudomallei, the etiologic agent of human melioidosis, is capable of causing severe acute infection with overwhelming septicemia leading to death. A high rate of recurrent disease occurs in adult patients, most often due to recrudesc...
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BIM promoter directly targeted by EBNA3C in polycomb-mediated repression by EBV.
Published: May, 2012

Abstract: Detailed analyses of the chromatin around the BIM promoter has revealed that latent Epstein-Barr virus (EBV) triggers the recruitment of polycomb repressive complex 2 (PRC2) core subunits and the trimethylation of histone H3 lysine 27 (H3K27me3) a...
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Hydroxylation of 5-methylcytosine by TET2 maintains the active state of the mammalian HOXA cluster.
Published: May, 2012

Abstract: Differentiation is accompanied by extensive epigenomic reprogramming, leading to the repression of stemness factors and the transcriptional maintenance of activated lineage-specific genes. Here we use the mammalian Hoxa cluster of developmental ge...
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Disruption of RAB40AL function leads to Martin-Probst syndrome, a rare X-linked multisystem neurodevelopmental human disorder.
Published: May, 2012

Abstract: Background and aim Martin-Probst syndrome (MPS) is a rare X-linked disorder characterised by deafness, cognitive impairment, short stature and distinct craniofacial dysmorphisms, among other features. The authors sought to identify the causative m...
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Can soy phytoestrogens decrease DNA methylation in BRCA1 and BRCA2 oncosuppressor genes in breast cancer?
Published: May, 2012

Abstract: Although soy phytoestrogens have been postulated to exert a protective effect against breast cancer, the attendant mechanisms, in particular epigenetics underpinnings, have remained elusive. We investigated the putative effects on DNA methylation ...
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Performance comparison of benchtop high-throughput sequencing platforms.
Published: April, 2012

Abstract: Three benchtop high-throughput sequencing instruments are now available. The 454 GS Junior (Roche), MiSeq (Illumina) and Ion Torrent PGM (Life Technologies) are laser-printer sized and offer modest set-up and running costs. Each instrument can gen...
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Development and Evaluation of a 9K SNP Array for Peach by Internationally Coordinated SNP Detection and Validation in Breeding Germplasm.
Published: April, 2012

Abstract: Although a large number of single nucleotide polymorphism (SNP) markers covering the entire genome are needed to enable molecular breeding efforts such as genome wide association studies, fine mapping, genomic selection and marker-assisted selecti...
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Breast Cancer Cells Induce Stromal Fibroblasts to Secrete ADAMTS1 for Cancer Invasion through an Epigenetic Change.
Published: April, 2012

Abstract: Microenvironment plays an important role in cancer development. We have reported that the cancer-associated stromal cells exhibit phenotypic and functional changes compared to stromal cells neighboring to normal tissues. However, the molecular mec...
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Complete Chloroplast Genome Sequence of an Orchid Model Plant Candidate: Erycina pusilla Apply in Tropical Oncidium Breeding.
Published: April, 2012

Abstract: Oncidium is an important ornamental plant but the study of its functional genomics is difficult. Erycina pusilla is a fast-growing Oncidiinae species. Several characteristics including low chromosome number, small genome size, short growth period,...
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Fast Homozygosity Mapping and Identification of a Zebrafish ENU-Induced Mutation by Whole-Genome Sequencing.
Published: April, 2012

Abstract: Forward genetics using zebrafish is a powerful tool for studying vertebrate development through large-scale mutagenesis. Nonetheless, the identification of the molecular lesion is still laborious and involves time-consuming genetic mapping. Here, ...
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Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk.
Published: March, 2012

Abstract: Cross-talk between DNA methylation and histone modifications drives the establishment of composite epigenetic signatures and is traditionally studied using correlative rather than direct approaches. Here we present sequential ChIP-bisulfite-sequen...
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DNA methylation dynamics, metabolic fluxes, gene splicing, and alternative phenotypes in honey bees.
Published: March, 2012

Abstract: In honey bees (Apis mellifera), the development of a larva into either a queen or worker depends on differential feeding with royal jelly and involves epigenomic modifications by DNA methyltransferases. To understand the role of DNA methylation in...
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Low-Dose Cd Induces Hepatic Gene Hypermethylation, along with the Persistent Reduction of Cell Death and Increase of Cell Proliferation in Rats and Mice.
Published: March, 2012

Abstract: BACKGROUND: Cadmium (Cd) is classified as a human carcinogen probably associated with epigenetic changes. DNA methylation is one of epigenetic mechanisms by which cells control gene expression. Therefore, the present study genome-widely screened t...
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Genetic and Epigenetic Determinants of Neurogenesis and Myogenesis.
Published: March, 2012

Abstract: The regulatory networks of differentiation programs have been partly characterized; however, the molecular mechanisms of lineage-specific gene regulation by highly similar transcription factors remain largely unknown. Here we compare the genome-wi...
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Methylome analysis using MeDIP-seq with low DNA concentrations.
Published: March, 2012

Abstract: DNA methylation is an epigenetic mark that has a crucial role in many biological processes. To understand the functional consequences of DNA methylation on phenotypic plasticity, a genome-wide analysis should be embraced. This in turn requires a t...
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Prenatal detection of aneuploidy and imbalanced chromosomal arrangements by massively parallel sequencing.
Published: February, 2012

Abstract: Fetal chromosomal abnormalities are the most common reasons for invasive prenatal testing. Currently, G-band karyotyping and several molecular genetic methods have been established for diagnosis of chromosomal abnormalities. Although these testing...
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Kinetics of DNA methylation inheritance by the Dnmt1-including complexes during the cell cycle.
Published: February, 2012

Abstract: ABSTRACT: BACKGROUND: The clonal transmission of lineage-specific DNA methylation patterns in a mammalian genome during the cellular division is a crucial biological process controlled by the DNA methyltransferase Dnmt1, mainly. To investigate pos...
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RHBDF2 mutations are associated with tylosis, a familial esophageal cancer syndrome.
Published: February, 2012

Abstract: Tylosis esophageal cancer (TOC) is an autosomal-dominant syndrome characterized by palmoplantar keratoderma, oral precursor lesions, and a high lifetime risk of esophageal cancer. We have previously localized the TOC locus to a small genomic inter...
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High-throughput molecular diagnosis of von Willebrand diseaseby next generation sequencing methods.
Published: February, 2012

Abstract: Genetic analysis of von Willebrand disease by von Willebrand factor gene sequencing has not yet become routine practice. Nevertheless, the prospects for molecular diagnosis have changed dramatically in recent years with the unveiling of next-gener...
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Three-dimensional folding and functional organization principles of the Drosophila genome.
Published: February, 2012

Abstract: Chromosomes are the physical realization of genetic information and thus form the basis for its readout and propagation. Here we present a high-resolution chromosomal contact map derived from a modified genome-wide chromosome conformation capture ...
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Serial translocation by means of circular intermediates underlies colour sidedness in cattle.
Published: February, 2012

Abstract: Colour sidedness is a dominantly inherited phenotype of cattle characterized by the polarization of pigmented sectors on the flanks, snout and ear tips. It is also referred to as 'lineback' or 'witrik' (which means white back), as colour-sided ani...
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Connexin 43 reverses malignant phenotypes of glioma stem cells by modulating E-cadherin.
Published: February, 2012

Abstract: Malfunctioned gap junctional intercellular communication (GJIC) has been thought associated with malignant transformation of normal cells. However, the role of GJIC-related proteins such as connexins in sustaining the malignant behavior of cancer ...
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Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer.
Published: February, 2012

Abstract: While genetic mutation is a hallmark of cancer, many cancers also acquire epigenetic alterations during tumorigenesis including aberrant DNA hypermethylation of tumor suppressors, as well as changes in chromatin modifications as caused by genetic ...
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Epigenetic regulation of the latency-associated region of Marek's disease virus in tumor-derived T-cell lines and primary lymphoma.
Published: February, 2012

Abstract: Meq is the major Marek's disease virus (MDV)-encoded oncoprotein and is essential for T-cell lymphomagenesis. Meq and several noncoding RNAs, including three microRNA (MiR) clusters, are expressed from the repeats of the MDV genome during latent i...
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Translocation capture sequencing: a method for high throughput mapping of chromosomal rearrangements.
Published: January, 2012

Abstract: Chromosomal translocations require formation and joining of DNA double strand breaks (DSBs). These events disrupt the integrity of the genome and are involved in producing leukemias, lymphomas and sarcomas. Translocations are frequent, clonal and ...
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Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression.
Published: January, 2012

Abstract: ABSTRACT: BACKGROUND: DNA cytosine methylation is an epigenetic modification that has been implicated in many biological processes. However, large-scale epigenomic studies have been applied to very few plant species, and variability in methylatio...
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RAD tag sequencing as a source of SNP markers in Cynara cardunculus L.
Published: January, 2012

Abstract: ABSTRACT: BACKGROUND: The globe artichoke (Cynara cardunculus L. var. scolymus) genome is relatively poorly explored, especially compared to those of the other major Asteraceae crops sunflower and lettuce. No SNP markers are in the public domain....
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Adaptation to P element transposon invasion in Drosophila melanogaster.
Published: December, 2011

Abstract: Transposons evolve rapidly and can mobilize and trigger genetic instability. Piwi-interacting RNAs (piRNAs) silence these genome pathogens, but it is unclear how the piRNA pathway adapts to invasion of new transposons. In Drosophila, piRNAs are en...
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Bio-CAP: a versatile and highly sensitive technique to purify and characterise regions of non-methylated DNA.
Published: December, 2011

Abstract: Across vertebrate genomes methylation of cytosine residues within the context of CpG dinucleotides is a pervasive epigenetic mark that can impact gene expression and has been implicated in various developmental and disease-associated processes. Se...
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DNA methylation regulates the expression of CXCL12 in rheumatoid arthritis synovial fibroblasts.
Published: December, 2011

Abstract: In the search for specific genes regulated by DNA methylation in rheumatoid arthritis (RA), we investigated the expression of CXCL12 in synovial fibroblasts (SFs) and the methylation status of its promoter and determined its contribution to the ex...
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A simple method for the parallel deep sequencing of full influenza A genomes.
Published: December, 2011

Abstract: Given the major threat of influenza A to human and animal health, and its ability to evolve rapidly through mutation and reassortment, tools that enable its timely characterization are necessary to help monitor its evolution and spread. For this p...
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Systematic comparison of three methods for fragmentation of long-range PCR products for next generation sequencing.
Published: November, 2011

Abstract: Next Generation Sequencing (NGS) technologies are gaining importance in the routine clinical diagnostic setting. It is thus desirable to simplify the workflow for high-throughput diagnostics. Fragmentation of DNA is a crucial step for preparation ...
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Distinct Epigenomic Features in End-Stage Failing Human Hearts
Published: November, 2011

Abstract: Background—The epigenome refers to marks on the genome, including DNA methylation and histone modifications, that regulate the expression of underlying genes. A consistent profile of gene expression changes in end-stage cardiomyopathy led us to hy...
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Rapid mapping and identification of mutations in Caenorhabditis elegans by restriction site-associated DNA mapping and genomic interval pull-down sequencing.
Published: November, 2011

Abstract: Forward genetic screens provide a powerful approach for inferring gene function on the basis of the phenotypes associated with mutated genes. However, determining the causal mutation by traditional mapping and candidate gene sequencing is often th...
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Pharmacodynamics of curcumin as DNA hypomethylation agent in restoring the expression of Nrf2 via promoter CpGs demethylation.
Published: November, 2011

Abstract: Prostate cancer (PCa) is one of the most deadly malignancies among men in the United States. Although localized prostate cancer can be effectively treated via surgery or radiation, metastatic disease is usually lethal. Recent evidence suggests tha...
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The draft genome and transcriptome of Cannabis sativa.
Published: October, 2011

Abstract: ABSTRACT: BACKGROUND: Cannabis sativa has been cultivated throughout human history as a source of fiber, oil and food, and for its medicinal and intoxicating properties. Selective breeding has produced cannabis plants for specific uses, including...
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Mutations in CSTA, encoding Cystatin A, underlie exfoliative ichthyosis and reveal a role for this protease inhibitor in cell-cell adhesion.
Published: October, 2011

Abstract: Autosomal-recessive exfoliative ichthyosis presents shortly after birth as dry, scaly skin over most of the body with coarse peeling of nonerythematous skin on the palms and soles, which is exacerbated by excessive moisture and minor trauma. Using...
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CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing.
Published: October, 2011

Abstract: Alternative splicing of pre-messenger RNA is a key feature of transcriptome expansion in eukaryotic cells, yet its regulation is poorly understood. Spliceosome assembly occurs co-transcriptionally, raising the possibility that DNA structure may di...
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Large-scale methylation domains mark a functional subset of neuronally expressed genes.
Published: October, 2011

Abstract: DNA methylation is essential for embryonic and neuronal differentiation, but the function of most genomic DNA methylation marks is poorly understood. Generally the human genome is highly methylated (>70%) except for CpG islands and gene promoters....
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Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing.
Published: October, 2011

Abstract: We applied a solution hybrid selection approach to the enrichment of CpG islands (CGIs) and promoter sequences from the human genome for targeted high-throughput bisulfite sequencing. A single lane of Illumina sequences allowed accurate and quanti...
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Translocation-capture sequencing reveals the extent and nature of chromosomal rearrangements in B lymphocytes.
Published: September, 2011

Abstract: Chromosomal rearrangements, including translocations, require formation and joining of DNA double strand breaks (DSBs). These events disrupt the integrity of the genome and are frequently involved in producing leukemias, lymphomas and sarcomas. De...
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High-throughput sequencing of complete human mtDNA genomes from the Caucasus and West Asia: high diversity and demographic inferences.
Published: September, 2011

Abstract: To investigate the demographic history of human populations from the Caucasus and surrounding regions, we used high-throughput sequencing to generate 147 complete mtDNA genome sequences from random samples of individuals from three groups from the...
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Exome sequencing identifies a DYNC1H1 mutation in a large pedigree with dominant axonal Charcot-Marie-Tooth disease.
Published: August, 2011

Abstract: Charcot-Marie-Tooth disease is characterized by length-dependent axonal degeneration with distal sensory loss and weakness, deep-tendon-reflex abnormalities, and skeletal deformities. It is caused by mutations in more than 40 genes. We investigate...
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Cell type-specific DNA methylation at intragenic CpG islands in the immune system.
Published: July, 2011

Abstract: Human and mouse genomes contain a similar number of CpG islands (CGIs), which are discrete CpG-rich DNA sequences associated with transcription start sites. In both species, ∼50% of all CGIs are remote from annotated promoters but, nevertheless, o...
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SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data.
Published: June, 2011

Abstract: BACKGROUND: The popularity of massively parallel exome and transcriptome sequencing projects demands new data mining tools with a comprehensive set of features to support a wide range of analysis tasks. RESULTS: SeqGene, a new data mining tool, su...
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Mutations in ZBTB24 are associated with immunodeficiency, centromeric instability, and facial anomalies syndrome type 2.
Published: June, 2011

Abstract: Autosomal-recessive immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome is mainly characterized by recurrent, often fatal, respiratory and gastrointestinal infections. About 50% of patients carry mutations in the DNA met...
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Human imprinted retrogenes exhibit non-canonical imprint chromatin signatures and reside in non-imprinted host genes.
Published: June, 2011

Abstract: Imprinted retrotransposed genes share a common genomic organization including a promoter-associated differentially methylated region (DMR) and a position within the intron of a multi-exonic 'host' gene. In the mouse, at least one transcript of the...
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Circumventing heterozygosity: sequencing the amplified genome of a single haploid Drosophila melanogaster embryo.
Published: June, 2011

Abstract: Heterozygosity is a major challenge to efficient, high-quality genomic assembly and to the full genomic survey of polymorphism and divergence. In Drosophila melanogaster lines derived from equatorial populations are particularly resistant to inbre...
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Analysis of the GAD1 promoter: trans-acting factors and DNA methylation converge on the 5' untranslated region.
Published: June, 2011

Abstract: GAD67 corresponds to one of two enzymes that decarboxylates glutamate to produce γ-aminobutyric acid, the main inhibitory neurotransmitter in the mammalian central nervous system, hence defining the cellular phenotype of a diverse set of inhibitor...
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Tumour evolution inferred by single-cell sequencing.
Published: April, 2011

Abstract: Genomic analysis provides insights into the role of copy number variation in disease, but most methods are not designed to resolve mixed populations of cells. In tumours, where genetic heterogeneity is common, very important information may be los...
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Tracing the domestication of a biofilm-forming bacterium.
Published: April, 2011

Abstract: Over the course of more than a century of laboratory experimentation, Bacillus subtilis has become "domesticated," losing its ability to carry out many behaviors characteristic of its wild ancestors. One such characteristic is the ability to form ...
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Epigenetic switch involved in activation of pioneer factor FOXA1-dependent enhancers.
Published: April, 2011

Abstract: Transcription factors (TFs) bind specifically to discrete regions of mammalian genomes called cis-regulatory elements. Among those are enhancers, which play key roles in regulation of gene expression during development and differentiation. Despite...
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Biparental inheritance of chromosomal abnormalities in male twins with non-syndromic mental retardation.
Published: March, 2011

Abstract: In a monozygotic twin couple with mental retardation (MR), we identified a maternally inherited inversion and a paternally inherited translocation: 46,XY,inv(10)(p11.2q21.2)mat,t(9;18)(p22;q21.1)pat. The maternally inherited inv(10) was a benign v...
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SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing.
Published: March, 2011

Abstract: The western black cottonwood (Populus trichocarpa) was the first tree to have its genome fully sequenced and has emerged as the model species for the study of secondary growth and wood formation. It is also a good candidate species for the product...
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DNA methyltransferase 1, cytosine methylation, and cytosine hydroxymethylation in mammalian mitochondria.
Published: March, 2011

Abstract: Mitochondrial DNA (mtDNA) has been reported to contain 5-methylcytosine (5mC) at CpG dinucleotides, as in the nuclear genome, but neither the mechanism generating mtDNA methylation nor its functional significance is known. We now report the presen...
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Multiplex target enrichment using DNA indexing for ultra-high throughput SNP detection.
Published: February, 2011

Abstract: Screening large numbers of target regions in multiple DNA samples for sequence variation is an important application of next-generation sequencing but an efficient method to enrich the samples in parallel has yet to be reported. We describe an adv...
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Comprehensive analysis of DNA-methylation in mammalian tissues using MeDIP-chip.
Published: February, 2011

Abstract: Genome-wide mapping of epigenetic changes is essential for understanding the mechanisms involved in gene regulation during cell differentiation and embryonic development. DNA-methylation is one of these key epigenetic marks that is directly linked...
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Local de novo assembly of RAD paired-end contigs using short sequencing reads.
Published: January, 2011

Abstract: Despite the power of massively parallel sequencing platforms, a drawback is the short length of the sequence reads produced. We demonstrate that short reads can be locally assembled into longer contigs using paired-end sequencing of restriction-si...
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Performance of microarray and liquid based capture methods for target enrichment for massively parallel sequencing and SNP discovery.
Published: January, 2011

Abstract: Targeted sequencing is a cost-efficient way to obtain answers to biological questions in many projects, but the choice of the enrichment method to use can be difficult. In this study we compared two hybridization methods for target enrichment for ...
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Affinity-based enrichment strategies to assay methyl-CpG binding activity and DNA methylation in early Xenopus embryos.
Published: January, 2011

Abstract: UNLABELLED: ABSTRACT: BACKGROUND: DNA methylation is a widespread epigenetic modification in vertebrate genomes. Genomic sites of DNA methylation can be bound by methyl-CpG-binding domain proteins (MBDs) and specific zinc finger proteins, which ca...
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Phenobarbital mediates an epigenetic switch at the constitutive androstane receptor (CAR) target gene Cyp2b10 in the liver of B6C3F1 mice.
Published: January, 2011

Abstract: Evidence suggests that epigenetic perturbations are involved in the adverse effects associated with some drugs and toxicants, including certain classes of non-genotoxic carcinogens. Such epigenetic changes (altered DNA methylation and covalent his...
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Enhanced chromatin accessibility and recruitment of JUNB mediate the sustained IL-4 expression in NFAT1 deficient T helper 2 cells.
Published: January, 2011

Abstract: Nuclear factor of activated T cells (NFAT) is a family of transcription factors composed of five proteins. Among them, NFAT1 is a predominant NFAT protein in CD4(+) T cells. NFAT1 positively regulates transcription of a large number of inducible c...
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RNA sequencing reveals two major classes of gene expression levels in metazoan cells.
Published: January, 2011

Abstract: The expression level of a gene is often used as a proxy for determining whether the protein or RNA product is functional in a cell or tissue. Therefore, it is of fundamental importance to understand the global distribution of gene expression level...
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Identification of novel SNPs in glioblastoma using targeted resequencing.
Published: January, 2011

Abstract: High-throughput sequencing opens avenues to find genetic variations that may be indicative of an increased risk for certain diseases. Linking these genomic data to other "omics" approaches bears the potential to deepen our understanding of pathoge...
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Global analysis of DNA methylation by methyl-capture sequencing reveals epigenetic control of Cisplatin resistance in ovarian cancer cell.
Published: January, 2011

Abstract: Cisplatin resistance is one of the major reasons leading to the high death rate of ovarian cancer. Methyl-Capture sequencing (MethylCap-seq), which combines precipitation of methylated DNA by recombinant methyl-CpG binding domain of MBD2 protein w...
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Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine.
Published: January, 2011

Abstract: In contrast to 5-methylcytosine (5-mC), which has been studied extensively, little is known about 5-hydroxymethylcytosine (5-hmC), a recently identified epigenetic modification present in substantial amounts in certain mammalian cell types. Here w...
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H2A.Z demarcates intergenic regions of the plasmodium falciparum epigenome that are dynamically marked by H3K9ac and H3K4me3.
Published: December, 2010

Abstract: Epigenetic regulatory mechanisms and their enzymes are promising targets for malaria therapeutic intervention; however, the epigenetic component of gene expression in P. falciparum is poorly understood. Dynamic or stable association of epigenetic ...
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Targets and dynamics of promoter DNA methylation during early mouse development.
Published: December, 2010

Abstract: DNA methylation is extensively reprogrammed during the early phases of mammalian development, yet genomic targets of this process are largely unknown. We optimized methylated DNA immunoprecipitation for low numbers of cells and profiled DNA methyl...
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Quality control and single nucleotide resolution analysis of methylated DNA immunoprecipitation products.
Published: December, 2010

Abstract: DNA methylation patterns are altered in many diseases, and their analysis has become of great interest. Methylated DNA immunoprecipitation (MeDIP) is a simple method to enrich the methylated fraction of the genome. However, it has been difficult t...
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Multiplexed DNA sequence capture of mitochondrial genomes using PCR products.
Published: November, 2010

Abstract: BACKGROUND: To utilize the power of high-throughput sequencers, target enrichment methods have been developed. The majority of these require reagents and equipment that are only available from commercial vendors and are not suitable for the target...
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Loss of H3 K79 trimethylation leads to suppression of Rtt107-dependent DNA damage sensitivity through the translesion synthesis pathway.
Published: November, 2010

Abstract: Genomic integrity is maintained by the coordinated interaction of many DNA damage response pathways, including checkpoints, DNA repair processes, and cell cycle restart. In Saccharomyces cerevisiae, the BRCA1 C-terminal domain-containing protein R...
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Whole-genome DNA methylation profiling using MethylCap-seq.
Published: November, 2010

Abstract: MethylCap-seq is a robust procedure for genome-wide profiling of DNA methylation. The approach consists of the capture of methylated DNA using the MBD domain of MeCP2, and subsequent next-generation sequencing of eluted DNA. Elution of the capture...
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High-resolution whole-genome sequencing reveals that specific chromatin domains from most human chromosomes associate with nucleoli.
Published: November, 2010

Abstract: The nuclear space is mostly occupied by chromosome territories and nuclear bodies. Although this organization of chromosomes affects gene function, relatively little is known about the role of nuclear bodies in the organization of chromosomal regi...
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Transcriptional profiling by deep sequencing identifies differences in mRNA transcript abundance in in vivo-derived versus in vitro-cultured porcine blastocyst stage embryos.
Published: November, 2010

Abstract: In vitro embryo culture systems promote development at rates lower than in vivo systems. The goal of this project was to discover transcripts that may be responsible for a decrease of embryo competency in blastocyst-stage embryos cultured in vitro...
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Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.
Published: October, 2010

Abstract: Analysis of DNA methylation patterns relies increasingly on sequencing-based profiling methods. The four most frequently used sequencing-based technologies are the bisulfite-based methods MethylC-seq and reduced representation bisulfite sequencing...
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Quantitative comparison of genome-wide DNA methylation mapping technologies.
Published: October, 2010

Abstract: DNA methylation plays a key role in regulating eukaryotic gene expression. Although mitotically heritable and stable over time, patterns of DNA methylation frequently change in response to cell differentiation, disease and environmental influences...
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Transcriptional profiling of day 12 porcine embryonic disc and trophectoderm samples using ultra-deep sequencing technologies.
Published: September, 2010

Abstract: cDNA derived from trophectoderm (TE) and embryonic disc (ED) of a single day 12 porcine embryo was subjected to next-generation sequencing using the Illumina platform. The short sequencing reads from triplicate sequencing runs were aligned to a cu...
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DNA methylation prevents CTCF-mediated silencing of the oncogene BCL6 in B cell lymphomas.
Published: August, 2010

Abstract: Aberrant DNA methylation commonly occurs in cancer cells where it has been implicated in the epigenetic silencing of tumor suppressor genes. Additional roles for DNA methylation, such as transcriptional activation, have been predicted but have yet...
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Terminal osseous dysplasia is caused by a single recurrent mutation in the FLNA gene.
Published: July, 2010

Abstract: Terminal osseous dysplasia (TOD) is an X-linked dominant male-lethal disease characterized by skeletal dysplasia of the limbs, pigmentary defects of the skin, and recurrent digital fibroma with onset in female infancy. After performing X-exome cap...
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Conserved role of intragenic DNA methylation in regulating alternative promoters.
Published: July, 2010

Abstract: Although it is known that the methylation of DNA in 5' promoters suppresses gene expression, the role of DNA methylation in gene bodies is unclear. In mammals, tissue- and cell type-specific methylation is present in a small percentage of 5' CpG i...
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Loss of Rb proteins causes genomic instability in the absence of mitogenic signaling.
Published: July, 2010

Abstract: Loss of G1/S control is a hallmark of cancer, and is often caused by inactivation of the retinoblastoma pathway. However, mouse embryonic fibroblasts lacking the retinoblastoma genes RB1, p107, and p130 (TKO MEFs) are still subject to cell cycle c...
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Use of Illumina sequencing to identify transposon insertions underlying mutant phenotypes in high-copy Mutator lines of maize.
Published: July, 2010

Abstract: High-copy transposons have been effectively exploited as mutagens in a variety of organisms. However, their utility for phenotype-driven forward genetics has been hampered by the difficulty of identifying the specific insertions responsible for ph...
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Estrogen-mediated epigenetic repression of large chromosomal regions through DNA looping.
Published: June, 2010

Abstract: The current concept of epigenetic repression is based on one repressor unit corresponding to one silent gene. This notion, however, cannot adequately explain concurrent silencing of multiple loci observed in large chromosome regions. The long-rang...
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Illumina sequencing library preparation for highly multiplexed target capture and sequencing.
Published: June, 2010

Abstract: The large amount of DNA sequence data generated by high-throughput sequencing technologies often allows multiple samples to be sequenced in parallel on a single sequencing run. This is particularly true if subsets of the genome are studied rather ...
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Massively parallel sequencing, a new method for detecting adventitious agents.
Published: May, 2010

Abstract: There has been an upsurge of interest in developing new veterinary and human vaccines and, in turn, this has involved the development of new mammalian and insect cell substrates. Excluding adventitious agents from these cells can be problematic, p...
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Targeted high throughput sequencing of a cancer-related exome subset by specific sequence capture with a fully automated microarray platform.
Published: April, 2010

Abstract: Sequence capture methods for targeted next generation sequencing promise to massively reduce cost of genomics projects compared to untargeted sequencing. However, evaluated capture methods specifically dedicated to biologically relevant genomic re...
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Unlocking short read sequencing for metagenomics.
Published: January, 2010

Abstract: BACKGROUND: Different high-throughput nucleic acid sequencing platforms are currently available but a trade-off currently exists between the cost and number of reads that can be generated versus the read length that can be achieved. METHODOLOGY/PR...
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Differential DNA methylation correlates with differential expression of angiogenic factors in human heart failure.
Published: January, 2010

Abstract: Epigenetic mechanisms such as microRNA and histone modification are crucially responsible for dysregulated gene expression in heart failure. In contrast, the role of DNA methylation, another well-characterized epigenetic mark, is unknown. In order...
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Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition.
Published: January, 2010

Abstract: We characterize and extend a highly efficient method for constructing shotgun fragment libraries in which transposase catalyzes in vitro DNA fragmentation and adaptor incorporation simultaneously. We apply this method to sequencing a human genome ...
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The epigenetic landscape of latent Kaposi sarcoma-associated herpesvirus genomes.
Published: January, 2010

Abstract: Herpesvirus latency is generally thought to be governed by epigenetic modifications, but the dynamics of viral chromatin at early timepoints of latent infection are poorly understood. Here, we report a comprehensive spatial and temporal analysis o...
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Monovalent and unpoised status of most genes in undifferentiated cell-enriched Drosophila testis.
Published: January, 2010

Abstract: BACKGROUND: Increasing evidence demonstrates that stem cells maintain their identities by a unique transcription network and chromatin structure. Opposing epigenetic modifications H3K27 me3 and H3K4 me3 have been proposed to label differentiation-...
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Genome-wide conserved consensus transcription factor binding motifs are hyper-methylated.
Published: January, 2010

Abstract: BACKGROUND: DNA methylation can regulate gene expression by modulating the interaction between DNA and proteins or protein complexes. Conserved consensus motifs exist across the human genome ("predicted transcription factor binding sites": "predic...
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Assessing the efficiency and significance of Methylated DNA Immunoprecipitation (MeDIP) assays in using in vitro methylated genomic DNA.
Published: January, 2010

Abstract: BACKGROUND: DNA methylation contributes to the regulation of gene expression during development and cellular differentiation. The recently developed Methylated DNA ImmunoPrecipitation (MeDIP) assay allows a comprehensive analysis of this epigeneti...
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Genome-wide analysis of allelic expression imbalance in human primary cells by high-throughput transcriptome resequencing.
Published: January, 2010

Abstract: Many disease-associated variants identified by genome-wide association (GWA) studies are expected to regulate gene expression. Allele-specific expression (ASE) quantifies transcription from both haplotypes using individuals heterozygous at tested ...
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Frequent long-range epigenetic silencing of protocadherin gene clusters on chromosome 5q31 in Wilms' tumor.
Published: November, 2009

Abstract: Wilms' tumour (WT) is a pediatric tumor of the kidney that arises via failure of the fetal developmental program. The absence of identifiable mutations in the majority of WTs suggests the frequent involvement of epigenetic aberrations in WT. We th...
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Microarray-based multicycle-enrichment of genomic subsets for targeted next-generation sequencing.
Published: September, 2009

Abstract: The lack of efficient high-throughput methods for enrichment of specific sequences from genomic DNA represents a key bottleneck in exploiting the enormous potential of next-generation sequencers. Such methods would allow for a systematic and targe...
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The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group.
Published: September, 2009

Abstract: We present the first Korean individual genome sequence (SJK) and analysis results. The diploid genome of a Korean male was sequenced to 28.95-fold redundancy using the Illumina paired-end sequencing method. SJK covered 99.9% of the NCBI human refe...
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Filter-based hybridization capture of subgenomes enables resequencing and copy-number detection.
Published: July, 2009

Abstract: To exploit contemporary sequencing technologies for targeted genetic analyses, we developed a hybridization enrichment strategy for DNA capture that uses PCR products as subgenomic traps. We applied this strategy to 115 kilobases of the human geno...
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Global analysis of DNA methylation and transcription of human repetitive sequences
Published: July, 2009

Abstract: Half of the human genome consists of repetitive DNA sequences. Recent studies in various organisms highlight the role of chromatin regulation of repetitive DNA in gene regulation as well as in maintainance of chromosomes and genome integrity. Henc...
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Improved Protocols for Illumina Sequencing
Published: July, 2009

Abstract: In this unit, we describe a set of improvements we have made to the standard Illumina protocols to make the sequencing process more reliable in a high-throughput environment, reduce amplification bias, narrow the distribution of insert sizes, and ...
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The reelin and GAD67 promoters are activated by epigenetic drugs that facilitate the disruption of local repressor complexes.
Published: February, 2009

Abstract: The epigenetic down-regulation of genes is emerging as a possible underlying mechanism of the GABAergic neuron dysfunction in schizophrenia. For example, evidence has been presented to show that the promoters associated with reelin and GAD67 are d...
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Hybrid selection of discrete genomic intervals on custom-designed microarrays for massively parallel sequencing.
Published: January, 2009

Abstract: Complementary techniques that deepen information content and minimize reagent costs are required to realize the full potential of massively parallel sequencing. Here, we describe a resequencing approach that directs focus to genomic regions of hig...
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Cell-free circulating DNA: diagnostic value in patients with testicular germ cell cancer.
Published: January, 2009

Abstract: PURPOSE: Increased levels of cell-free circulating DNA have been described in various malignancies as a diagnostic and prognostic biomarker. We analyzed the significance of cell-free DNA in patients with testicular cancer. MATERIALS AND METHODS: C...
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Methylated DNA immunoprecipitation and microarray-based analysis: detection of DNA methylation in breast cancer cell lines.
Published: January, 2009

Abstract: The methylated DNA immunoprecipitation microarray (MeDIP-chip) is a genome-wide, high-resolution approach to detect DNA methylation in whole genome or CpG (cytosine base followed by a guanine base) islands. The method utilizes anti-methylcytosine ...
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Improving the efficiency of genomic loci capture using oligonucleotide arrays for high throughput resequencing.
Published: January, 2009

Abstract: BACKGROUND: The emergence of next-generation sequencing technology presents tremendous opportunities to accelerate the discovery of rare variants or mutations that underlie human genetic disorders. Although the complete sequencing of the affected ...
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A link between RNA metabolism and silencing affecting Arabidopsis development.
Published: June, 2008

Abstract: MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) are abundant endogenous small RNAs (smRNAs) that control transcript expression through posttranscriptional gene silencing. Here, we show that concomitant loss of XRN4/EIN5, a 5'-3' exoribonucl...
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Highly integrated single-base resolution maps of the epigenome in Arabidopsis.
Published: May, 2008

Abstract: Deciphering the multiple layers of epigenetic regulation that control transcription is critical to understanding how plants develop and respond to their environment. Using sequencing-by-synthesis technology we directly sequenced the cytosine methy...
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Inactivation of a Human Kinetochore by Specific Targeting of Chromatin Modifiers
Published: April, 2008

Abstract: We have used a human artificial chromosome (HAC) to manipulate the epigenetic state of chromatin within an active kinetochore. The HAC has a dimeric α-satellite repeat containing one natural monomer with a CENP-B binding site, and one completely a...
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Post-mortem genetic analysis in juvenile cases of sudden cardiac death

Abstract: Background The reason behind a sudden death of a young individual remains unknown in up to 50% of postmortem cases. Pathogenic mutations in genes encoding heart proteins are known to cause sudden cardiac death. Objective The aim of our study was...
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Experimental Study on Malignant Transformation of Human Bronchial Epithelial Cells Induced by Glycidyl Methacrylate and Analysis on its Methylation

Abstract: Objective To establish the model of human bronchial epithelial cells(16HBE) malignant transformation induced by glycidyl methacrylate(GMA) and define the different methylation genes at different stages. Methods DNA was extracted at different 16...
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A novel method for the genome-wide high resolution analysis of DNA damage.

Abstract: DNA damage occurs via endogenous and exogenous genotoxic agents and compromises a genome's integrity. Knowing where damage occurs within a genome is crucial to understanding the repair mechanisms which protect this integrity. This paper describes ...
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Oxyphil Cell Metaplasia in the Parathyroids Is Characterized by Somatic Mitochondrial DNA Mutations in NADH Dehydrogenase Genes and Cytochrome c Oxidase Activity–Impairing Genes

Abstract: Oxyphil cell transformation of epithelial cells due to the accumulation of mitochondria occurs often during cellular aging. To understand the pathogenic mechanisms, we studied mitochondrial DNA (mtDNA) alterations in the three cell types of the pa...
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AutoMeDIP-seq: A high-throughput, whole genome, DNA methylation assay

Abstract: DNA methylation is an epigenetic mark linking DNA sequence and transcription regulation, and therefore plays an important role in phenotypic plasticity. The ideal whole genome methylation (methylome) assay should be accurate, affordable, high-thro...
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Alterations of the RRAS and ERCC1 Genes at 19q13 in Gemistocytic Astrocytomas.

Abstract: Gemistocytic astrocytoma (World Health Organization grade II) is a rare variant of diffuse astrocytoma that is characterized by the presence of neoplastic gemistocytes and has a significantly less favorable prognosis. Other than frequent TP53 muta...
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Low dose effects of dichlorodiphenyltrichloroethane (DDT) on gene transcription and DNA methylation in the hypothalamus of young male rats: implication of hormesis-like effects.

Abstract: To verify the relationship between oxidative stress and DNA methylation in the young brain, dichlorodiphenyltrichloroethane (DDT) was administered by gavage to male young rats at doses of 0, 0.006, 0.06, 0.6, 6, and 60 mg/kg/day for a period of 4 ...
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Genetic Screens for Floral Mutants in Arabidopsis thaliana: Enhancers and Suppressors

Abstract: The flower is a hallmark feature that has contributed to the evolutionary success of land plants. Diverse mutagenic agents have been employed as a tool to genetically perturb flower development and identify genes involved in floral patterning and ...
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Exome sequencing reveals new insights into the progression of abdominal aortic aneurysm.

Abstract: BACKGROUND: Abdominal aortic aneurysm (AAA) is a multi-factorial disease and its underlying pathogenesis remains poorly understood. AIM: We aim to search for the underlying etiology of AAA using whole exome sequencing and gene expression analysi...
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SNP Discovery and Genotyping for Evolutionary Genetics Using RAD Sequencing

Abstract: Next-generation sequencing technologies are revolutionizing the field of evolutionary biology, opening the possibility for genetic analysis at scales not previously possible. Research in population genetics, quantitative trait mapping, comparative...
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Clinical and public health research using methylated DNA immunoprecipitation (MeDIP) A comparison of commercially available kits to examine differential DNA methylation across the genome

Abstract: The methylated DNA immunoprecipitation method (MeDIP) is a genome-wide, high-resolution approach that detects DNA methylation with oligonucleotide tiling arrays or high throughput sequencing platforms. A simplified highthroughput MeDIP assay will ...
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High-throughput whole-genome sequencing of E14 mouse embryonic stem cells

Abstract: Mouse E14 embryonic stem cells (ESCs) are the most used ESC line, often employed for genome-wide studies involving next generation sequencing analysis [1 – 5] . More than 2 × 10 E9 sequences made on Illumina platform derivedfromthegenomeofE14embry...
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Deletion of the de novo DNA methyltransferase Dnmt3a promotes lung tumor progression.

Abstract: Alterations in DNA methylation have been associated with genome-wide hypomethylation and regional de novo methylation in numerous cancers. De novo methylation is mediated by the de novo methyltransferases Dnmt3a and 3b, but only Dnmt3b has been im...
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Methylation analysis by microarray.

Abstract: Differential methylation hybridization (DMH) is a high-throughput DNA methylation screening tool that utilizes methylation-sensitive restriction enzymes to profile methylated fragments by hybridizing them to a CpG island microarray. This array con...
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Library preparation and data analysis packages for rapid genome sequencing.

Abstract: High-throughput sequencing (HTS) has quickly become a valuable tool for comparative genetics and genomics and is now regularly carried out in laboratories that are not connected to large sequencing centers. Here we describe an updated version of o...
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Short-read DNA Sequencing Yields Microsatellite Markers for Rheum

Abstract: Identifying and evaluating genetic diversity of culinary rhubarb (Rheum ×rhababarum) cultivars using morphological characteristics is challenging given the existence of synonyms and nomenclatural inconsistencies. Some cultivars with similar names ...
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Broad spectrum microarray for fingerprint-based bacterial species identification.

Abstract: BACKGROUND: Microarrays are powerful tools for DNA-based molecular diagnostics and identification of pathogens. Most target a limited range of organisms and are based on only one or a very few genes for specific identification. Such microarrays ar...
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Detection of DNA methylation by MeDIP and MBDCap assays: an overview of techniques.

Abstract: DNA methylation has been characterized as the representative example of epigenetic modifications and implicated in numerous biological processes, such as genomic imprinting and X chromosome inactivation. It primarily occurs at CpG dinucleotides in...
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Mapping replication origin sequences in eukaryotic chromosomes.

Abstract: Recent advances in genome-sequencing technology have led to the complete mapping of DNA replication initiation sites in the human genome. This thorough origin mapping facilitates understanding of the relationship between replication initiation eve...
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Consistency of metagenomic assignment programs in simulated and real data.

Abstract: BACKGROUND: Metagenomics is the genomic study of uncultured environmental samples, which has been greatly facilitated by the advent of shotgun-sequencing technologies. One of the main focuses of metagenomics is the discovery of previously uncultur...
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TET1 regulates hypoxia-induced epithelial-mesenchymal transition by acting as a co-activator.

Abstract: BACKGROUND: Hypoxia induces the epithelial-mesenchymal transition, EMT, to promote cancer metastasis. In addition to transcriptional regulation mediated by hypoxia-inducible factors, HIFs, other epigenetic mechanisms of gene regulation, such as hi...
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Methylated DNA Immunoprecipitation (MeDIP) from Low Amounts of Cells.

Abstract: Methylated DNA immunoprecipitation (MeDIP) is an immunocapturing approach for unbiased enrichment of DNA that is methylated on cytosines. The principle is that genomic DNA is randomly sheared by sonication and immunoprecipitated with an antibody t...
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Genome-wide methylation profiling reveals Zinc finger protein 516 (ZNF516) and FK-506-binding protein 6 (FKBP6) promoters frequently methylated in cervical neoplasia, associated with HPV status and ethnicity in a Chilean population.

Abstract: Cervical cancer is a major health concern among women in Latin America due to its high incidence and mortality. Therefore, the discovery of molecular markers for cervical cancer screening and triage is imperative. The aim of this study was to use ...
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Diagnostic applications of next generation sequencing: working towards quality standards

Abstract: Over the past 6 years, next generation sequencing (NGS) has been established as a valuable high-throughput method for research in molecular genetics and has successfully been employed in the identification of rare and common genetic variations. Al...
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Enrichment of Methylated DNA by Methyl-CpG Immunoprecipitation.

Abstract: Normal DNA methylation is an epigenetic modification required for proper development. Aberrant DNA methylation, in contrast, is frequently observed in many different malignancies including leukemias and lymphomas. Global DNA methylation profiling ...
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