Cell-free DNA methylome profiling by MBD-seq with ultra-low input
Jinyong Huang, Alex C. Soupir & Liang Wang
Methylation signatures in cell-free DNA (cfDNA) have shown great sensitivity and specificity in the characterization of tumour status and classification of tumour types, as well as the response to therapy and recurrence. Currently, most cfDNA methylation studies are based on bisulphite conversion, especially targete...
Genome-wide DNA methylation and RNA-seq analyses identify genes andpathways associated with doxorubicin resistance in a canine diffuse largeB-cell lymphoma cell line.
Hsu, C.-H. et al.
Doxorubicin resistance is a major challenge in the successful treatment of canine diffuse large B-cell lymphoma (cDLBCL). In the present study, MethylCap-seq and RNA-seq were performed to characterize the genome-wide DNA methylation and differential gene expression patterns respectively in CLBL-1 8.0, a doxorubicin-...
Genome-wide DNA methylation analysis using MethylCap-seq in caninehigh-grade B-cell lymphoma.
Hsu, Chia-Hsin and Tomiyasu, Hirotaka and Lee, Jih-Jong and Tung, Chun-Weiand Liao, Chi-Hsun and Chuang, Cheng-Hsun and Huang, Ling-Ya and Liao,Kuang-Wen and Chou, Chung-Hsi and Liao, Albert T C and Lin, Chen-Si
DNA methylation is a comprehensively studied epigenetic modification and plays crucial roles in cancer development. In the present study, MethylCap-seq was used to characterize the genome-wide DNA methylation patterns in canine high-grade B-cell lymphoma (cHGBL). Canine methylated DNA fragments were captured and the...
Benchmarking DNA methylation assays in a reef-building coral.
Dixon, Groves and Matz, Mikhail
Interrogation of chromatin modifications, such as DNA methylation, has the potential to improve forecasting and conservation of marine ecosystems. The standard method for assaying DNA methylation (whole genome bisulphite sequencing), however, is currently too costly to apply at the scales required for ecological res...
Targeting DNA methylation depletes uterine leiomyoma stem-cell enrichedpopulation by stimulating their differentiation.
Liu, S and Yin, P and Xu, J and Dotts, AJ and Kujawa, SA and Coon, VJS and Zhao, H and Hilatifard, AS and Dai, Y and Bulun, SE
Uterine leiomyoma is the most common tumor in women and can cause severe morbidity. Leiomyoma growth requires maintenance and proliferation of a stem cell population. Dysregulated DNA methylation has been reported in leiomyoma, but its role in leiomyoma stem cell regulation remains unclear. Here, we FACS sorted cell...
DNA methylation dynamics underlie metamorphic gene regulation programs in Xenopus tadpole brain.
Kyono Y, Raj S, Sifuentes CJ, Buisine N, Sachs L, Denver RJ
Methylation of cytosine residues in DNA influences chromatin structure and gene transcription, and its regulation is crucial for brain development. There is mounting evidence that DNA methylation can be modulated by hormone signaling. We analyzed genome-wide changes in DNA methylation and their relationship to gene ...
SMaSH: Sample matching using SNPs in humans.
Westphal M, Frankhouser D, Sonzone C, Shields PG, Yan P, Bundschuh R
BACKGROUND: Inadvertent sample swaps are a real threat to data quality in any medium to large scale omics studies. While matches between samples from the same individual can in principle be identified from a few well characterized single nucleotide polymorphisms (SNPs), omics data types often only provide low to mod...
Increased presence and differential molecular imprinting of transit amplifying cells in psoriasis.
Witte K, Jürchott K, Christou D, Hecht J, Salinas G, Krüger U, Klein O, Kokolakis G, Witte-Händel E, Mössner R, Volk HD, Wolk K, Sabat R
Psoriasis is a very common chronic inflammatory skin disease characterized by epidermal thickening and scaling resulting from keratinocyte hyperproliferation and impaired differentiation. Pathomechanistic studies in psoriasis are often limited by using whole skin tissue biopsies, neglecting their stratification and ...
Plasticity of histone modifications around Cidea and Cidec genes with secondary bile in the amelioration of developmentally-programmed hepatic steatosis.
Urmi JF, Itoh H, Muramatsu-Kato K, Kohmura-Kobayashi Y, Hariya N, Jain D, Tamura N, Uchida T, Suzuki K, Ogawa Y, Shiraki N, Mochizuki K, Kubota T, Kanayama N
We recently reported that a treatment with tauroursodeoxycholic acid (TUDCA), a secondary bile acid, improved developmentally-deteriorated hepatic steatosis in an undernourishment (UN, 40% caloric restriction) in utero mouse model after a postnatal high-fat diet (HFD). We performed a microarray analysis and focused ...
Role of gene body methylation in acclimatization and adaptation in a basalmetazoan.
Dixon, Groves and Liao, Yi and Bay, Line K and Matz, Mikhail V
Gene body methylation (GBM) has been hypothesized to modulate responses to environmental change, including transgenerational plasticity, but the evidence thus far has been lacking. Here we show that coral fragments reciprocally transplanted between two distant reefs respond predominantly by increase or decrease in g...
DNA Methylation and Regulatory Elements during Chicken Germline Stem Cell Differentiation.
He Y, Zuo Q, Edwards J, Zhao K, Lei J, Cai W, Nie Q, Li B, Song J
The production of germ cells in vitro would open important new avenues for stem biology and human medicine, but the mechanisms of germ cell differentiation are not well understood. The chicken, as a great model for embryology and development, was used in this study to help us explore its regulatory mechanisms. ...
Antioxydation And Cell Migration Genes Are Identified as Potential Therapeutic Targets in Basal-Like and BRCA1 Mutated Breast Cancer Cell Lines
Privat M. et al.
Basal-like breast cancers are among the most aggressive cancers and effective targeted therapies are still missing. In order to identify new therapeutic targets, we performed Methyl-Seq and RNA-Seq of 10 breast cancer cell lines with different phenotypes. We confirmed that breast cancer subtypes cluster the RNA-Seq ...
Gene body methylation is involved in coarse genome-wide adjustment of gene expression during acclimatization
Groves Dixon1, Yi Liao1, Line K. Bay2 and Mikhail V. Matz
Gene body methylation (GBM) is a taxonomically widespread epigenetic modification of the DNA the function of which remains unclear 1,2. GBM is bimodally distributed among genes: it is high in ubiquitously expressed housekeeping genes and low in context-dependent inducible genes 2,3, and it has been hypothesized that...
Methylome analysis of extreme chemoresponsive patients identifies novel markers of platinum sensitivity in high-grade serous ovarian cancer
Tomar T. et al.
Despite an early response to platinum-based chemotherapy in advanced stage high-grade serous ovarian cancer (HGSOC), the majority of patients will relapse with drug-resistant disease. Aberrant epigenetic alterations like DNA methylation are common in HGSOC. Differences in DNA methylation are associate...
ALDH1A3 is epigenetically regulated during melanocyte transformation and is a target for melanoma treatment
Pérez-Alea M. et al.
Despite the promising targeted and immune-based interventions in melanoma treatment, long-lasting responses are limited. Melanoma cells present an aberrant redox state that leads to the production of toxic aldehydes that must be converted into less reactive molecules. Targeting the detoxification machinery constitut...
Male fertility status is associated with DNA methylation signatures in sperm and transcriptomic profiles of bovine preimplantation embryos
Kropp J. et al.
Infertility in dairy cattle is a concern where reduced fertilization rates and high embryonic loss are contributing factors. Studies of the paternal contribution to reproductive performance are limited. However, recent discoveries have shown that, in addition to DNA, sperm delivers transcription facto...
Comparative analysis of MBD-seq and MeDIP-seq and estimation of gene expression changes in a rodent model of schizophrenia
Neary J.L. et al.
We conducted a comparative study of multiplexed affinity enrichment sequence methodologies (MBD-seq and MeDIP-seq) in a rodent model of schizophrenia, induced by in utero methylazoxymethanol acetate (MAM) exposure. We also examined related gene expression changes using a pooled sample approach. MBD-seq and MeDIP-seq...
Conserved effect of aging on DNA methylation and association with EZH2 polycomb protein in mice and humans.
Mozhui K. and Pandey A.K.
In humans, DNA methylation at specific CpG sites can be used to estimate the 'epigenetic clock', a biomarker of aging and health. The mechanisms that regulate the aging epigenome and level of conservation are not entirely clear. We performed affinity-based enrichment with methyl-CpG binding domain protein followed b...
Epigenetic sampling effects: nephrectomy modifies the clear cell renal cell cancer methylome
Van Neste C. et al.
Currently, it is unclear to what extent sampling procedures affect the epigenome. Here, this phenomenon was evaluated by studying the impact of artery ligation on DNA methylation in clear cell renal cancer.
DNA methylation profiles between vascularised tumour biopsy samples and devascularise...
Determinants of orofacial clefting II: Effects of 5-Aza-2′-deoxycytidine on gene methylation during development of the first branchial arch
Seelan R.S. et al.
Defects in development of the secondary palate, which arise from the embryonic first branchial arch (1-BA), can cause cleft palate (CP). Administration of 5-Aza-2′-deoxycytidine (AzaD), a demethylating agent, to pregnant mice on gestational day 9.5 resulted in complete penetrance of CP in fetuses. Several gene...
Evolutionary Consequences of DNA Methylation in a Basal Metazoan.
Dixon, Groves B and Bay, Line K and Matz, Mikhail V
Gene body methylation (gbM) is an ancestral and widespread feature in Eukarya, yet its adaptive value and evolutionary implications remain unresolved. The occurrence of gbM within protein-coding sequences is particularly puzzling, because methylation causes cytosine hypermutability and hence is likely to produce del...
Comparative DNA Methylation and Gene Expression Analysis Identifies Novel Genes for Structural Congenital Heart Diseases
Grunert M et al.
Aims For the majority of congenital heart diseases (CHDs), the full complexity of the causative molecular network, which is driven by genetic, epigenetic and environmental factors, is yet to be elucidated. Epigenetic alterations are suggested to play a pivotal role in modulating the phenotypic expression of CHDs a...
Molecular and epigenetic features of melanomas and tumor immune microenvironment linked to durable remission to ipilimumab - based immunotherapy in metastatic patients
Seremet T et al.
Ipilimumab (Ipi) improves the survival of advanced melanoma patients with an incremental long-term benefit in 10–15 % of patients. A tumor signature that correlates with this survival benefit could help optimizing individualized treatment strategies.
Freshly frozen melanoma met...
Integrative epigenomic analysis reveals unique epigenetic signatures involved in unipotency of mouse female germline stem cells
Zhang XL et al.
Germline stem cells play an essential role in establishing the fertility of an organism. Although extensively characterized, the regulatory mechanisms that govern the fundamental properties of mammalian female germline stem cells remain poorly understood.
We generate genome-wide profiles ...
RAB25 expression is epigenetically downregulated in oral and oropharyngeal squamous cell carcinoma with lymph node metastasis
Clausen MJ et al.
Oral and oropharyngeal squamous cell carcinoma (OOSCC) have a low survival rate, mainly due to metastasis to the regional lymph nodes. For optimal treatment of these metastases, a neck dissection is required; however, inaccurate detection methods results in under- and over-treatment. New DNA prognostic methylation b...
Genic DNA methylation drives codon bias in stony corals
Dixon G et al.
Gene body methylation (gbM) is an ancestral and widespread feature in Eukarya, yet its adaptive value and evolutionary implications remain unresolved. The occurrence of gbM within protein coding sequences is particularly puzzling, because methylation causes cytosine hypermutability and hence is likely to produce del...
A genome-wide search for eigenetically regulated genes in zebra finch using MethylCap-seq and RNA-seq
Sandra Steyaert, Jolien Diddens, Jeroen Galle, Ellen De Meester, Sarah De Keulenaer, Antje Bakker, Nina Sohnius-Wilhelmi, Carolina Frankl-Vilches, Annemie Van der Linden, Wim Van Criekinge, Wim Vanden Berghe & Tim De Meyer
Learning and memory formation are known to require dynamic CpG (de)methylation and gene expression changes. Here, we aimed at establishing a genome-wide DNA methylation map of the zebra finch genome, a model organism in neuroscience, as well as identifying putatively epigenetically regulated genes. RNA- and MethylCa...
DNA methylation profiling of primary neuroblastoma tumors using methyl-CpG-binding domain sequencing
Decock A et al.
Comprehensive genome-wide DNA methylation studies in neuroblastoma (NB), a childhood tumor that originates from precursor cells of the sympathetic nervous system, are scarce. Recently, we profiled the DNA methylome of 102 well-annotated primary NB tumors by methyl-CpG-binding domain (MBD) sequencing, in order to ide...
Identification and validation of WISP1 as an epigenetic regulator of metastasis in oral squamous cell carcinoma
Clausen MJ, Melchers LJ, Mastik MF, Slagter-Menkema L, Groen HJ, van der Laan BF, van Criekinge W, de Meyer T, Denil S, Wisman GB, Roodenburg JL, Schuuring E
Lymph node (LN) metastasis is the most important prognostic factor in oral squamous cell carcinoma (OSCC) patients. However, in approximately one third of OSCC patients nodal metastases remain undetected, and thus are not adequately treated. Therefore, clinical assessment of LN metastasis needs to be improved. The p...
DNA methylation in an engineered heart tissue model of cardiac hypertrophy: common signatures and effects of DNA methylation inhibitors
Stenzig J et al.
DNA methylation affects transcriptional regulation and constitutes a drug target in cancer biology. In cardiac hypertrophy, DNA methylation may control the fetal gene program. We therefore investigated DNA methylation signatures and their dynamics in an in vitro model of cardiac hypertrophy based on engineered heart...
∆ DNMT3B4-del Contributes to Aberrant DNA Methylation Patterns in Lung Tumorigenesis
Mark Z. Ma, Ruxian Lin, José Carrillo, Manisha Bhutani, Ashutosh Pathak, Hening Ren, Yaokun Li, Jiuzhou Song, Li Mao
Aberrant DNA methylation is a hallmark of cancer but mechanisms contributing to the abnormality remain elusive. We have previously shown that ∆DNMT3B is the predominantly expressed form of DNMT3B. In this study, we found that most of the lung cancer cell lines tested predominantly expressed DNMT3B isoforms without e...
Prenatal Exposure to DEHP Affects Spermatogenesis and Sperm DNA Methylation in a Strain-Dependent Manner.
Prados J, Stenz L, Somm E, Stouder C, Dayer A, Paoloni-Giacobino A
Di-(2-ethylhexyl)phtalate (DEHP) is a plasticizer with endocrine disrupting properties found ubiquitously in the environment and altering reproduction in rodents. Here we investigated the impact of prenatal exposure to DEHP on spermatogenesis and DNA sperm methylation in two distinct, selected, and sequenced mice st...
Quality evaluation of methyl binding domain based kits for enrichment DNA-methylation sequencing.
De Meyer T, Mampaey E, Vlemmix M, Denil S, Trooskens G, Renard JP, De Keulenaer S, Dehan P, Menschaert G, Van Criekinge W
DNA-methylation is an important epigenetic feature in health and disease. Methylated sequence capturing by Methyl Binding Domain (MBD) based enrichment followed by second-generation sequencing provides the best combination of sensitivity and cost-efficiency for genome-wide DNA-methylation profiling. However, existin...