Diagenode

IP-Star® Compact Automated System

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Catalog Number
Format
B03000002
(UH-002-0001)
1 unit

The IP-Star® Compact Automated System provides the flexibility needed to change multiple parameters in the protocols to achieve optimal experimental conditions. Samples generated on the system are compatible with popular downstream applications such as qPCR, microarrays and next generation sequencing platforms. In addition to automated ChIP and DNA methylation protocols, this system contains a wide variety of protocols including next generation sequencing library preparation and sample purification.

PUBLICATION

Epigenetic dynamics of monocyte-to-macrophage differentiation

BACKGROUND:

Monocyte-to-macrophage differentiation involves major biochemical and structural changes. In order to elucidate the role of gene regulatory changes during this process, we used high-throughput sequencing to analyze the complete transcriptome and epigenome of human monocytes that were differentiated in vitro by addition of colony-stimulating factor 1 in serum-free medium.

RESULTS:

Numerous mRNAs and miRNAs were significantly up- or down-regulated. More than 100 discrete DNA regions, most often far away from transcription start sites, were rapidly demethylated by the ten eleven translocation enzymes, became nucleosome-free and gained histone marks indicative of active enhancers. These regions were unique for macrophages and associated with genes involved in the regulation of the actin cytoskeleton, phagocytosis and innate immune response.

CONCLUSIONS:

In summary, we have discovered a phagocytic gene network that is repressed by DNA methylation in monocytes and rapidly de-repressed after the onset of macrophage differentiation.

read more.

Wallner S et al.

  • Case study
    CASE STUDY

    Columbia University - Transcription Factor ChIP-seq with 10 times less input

    Katia Basso at Columbia University demonstrated that the Microplex NGS Library Preparation Kit is an optimal solution for low input ChIP-seq of transcription factors. Her study demonstrated:

    • TF ChIP-seq using 10 times less input than a standard ChIP-seq
    • High reproducibility of transcription factor ChIP-seq from only 1,000,000 cells
    • The simplicity of the 3-step MicroPlex Kit protocol with NO intermediate purifications
    • Walk away automation with the IP-Star®
    Low input transcription factor ChIP-seq

    BCL6 binding on CD69 promoter. B cell lymphoma cell line P3HR1 was crosslinked and then sonicated using the Bioruptor® Pico. ChIP was performed on the IP-Star® Automation instrument. The MicroPlex v2 Kit from Diagenode was used for library preparation. The plots represent raw reads, the squares below the plots mark the significantly enriched peaks (according to the peak call software). Red box: peak regions that have been previously demonstrated by independent assays to be enriched for BCL6 binding. Data courtesy of Katia Basso, Columbia University, New York.

  • Testimonials

    The ability to produce libraries starting with low input DNA is primordial when using ChIP-seq. I am a ChIP-seq user and I always use the MicroPlex kit for library making from my immunoprecipitated DNA. Not only it’s quick and requires as little as 50 pg of input DNA but it also never fails. I’ve made over 100 libraries using the MicroPlex library preparation kit, and none of them failed. I use the Microplex kit for preparing libraries from immunoprecipitated DNA and from genomic DNA with low concentration.
    As part of a genomics lab, I regularly prepare libraries from a large number of samples. The IP-star® is extremely useful for high throughput library preparation. I have prepared 200 genomic libraries in less than 1 month using the IP-star®, it has helped me economize time and effort and increase reproducibility. I have used the IP-star® for automation of ChIP as well; 16 samples can be processed in one run. In brief, it’s a blessing to have this machine if you apply ChIP-seq to a large number of samples.

    Zineb Rchiad, Microbial Genomics Laboratory, King Abdullah University of Science and Technology, Kingdom of Saudi Arabia.

    Automated ChIP experiments in the IP-Star® Compact Automated System can be used to detect changes in transcription factor binding after treatment with small interference RNAs. Compared to conventionnal ChIP, the use of the SX-8G IP-Star® Compact in combination with the Auto ChIP kit saves working time and improves the reproducibility of ChIP experiments

    S. Prall, Northern Institute of Cancer Research, Newcastle University

    We found that the IP-Star® provides an efficient, reliable and accurate tool for the construction of Illumina next-generation RNA-seq libraries, especially for trancriptome-based annotation of larger genomes or genomes with many alternative gene isoforms. The automated protocol significantly saves on-hands experimentation time, related costs and error-prone manual steps. Added benefits include ease of operation and generation of consistent data regardless of human variability and experimental run. Adaptation of this technology should support the unveiling of the mechanisms governing differential gene expression and transcription processing genome-wide, leading to a better understanding of genetic and epigenetic regulation and inheritance in a time-efficient manner.

    UB Genomics and Bioinformatics Core, State University of New York at Buffalo, Research Team: Dr N. Nowak, Dr M.J. Buck, Dr M. Tsompana, S. Valiyaparambil, J. Bard, and B. Marzullo.

    Not only does the IP-Star eliminate the problem of human variation associated with producing our samples, it also enables us to produce 1000-2000 ChIP-seq samples per year very reliably. The IP-Star reduces our processing time down from one day of manual work to just one overnight run with only 30 minutes of hands-on work. The IP-Star has made all our ChIPs consistent and the process completely reliable regardless of the operator or the time of day

    Dr. John Lambourne, Postdoctorate Researcher at the Innovation Centre, McGill University, Canada

    We are very happy with the SX-8G IP-Star that we are routinely using in combination with MeDIP or MethylCap for DNA methylation profiling or for ChIP of histones or transcription factors. The use of the robot significantly reduces the hands-on time, and even more importantly provides a very high reproducibility, which is very valuable and essential for the generation of large number numbers of precious samples that will be analyzed on NGS platforms

    Henk Stunnenberg, The Radboud University Nijmegen Medical Centre

    In life sciences, epigenetics is nowadays the most rapid developing field with new astonishing discoveries made every day. To keep pace with this field, we are in need of reliable tools to foster our research - tools Diagenode provides us with. From antibodies to automated solutions - all from one source and with robust support. Antibodies used in our lab: H3K27me3 polyclonal antibody – Premium, H3K4me3 polyclonal antibody – Premium, H3K9me3 polyclonal antibody – Premium, H3K4me1 polyclonal antibody – Premium, CTCF polyclonal antibody – Classic, Rabbit IgG.

    Dr. Florian Uhle, Dept. of Anesthesiology, Heidelberg University Hospital, Germany
  • Protocols
    AMPure® XP Size Selection - IP-Star Compact
    The “AMPure XP Size Selection” protocol on the IP-Star® is using the standard &ld...
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    AMPure® XP Size Selection - IP-Star® Compact -
    The “AMPure_XP_Size_Selection” protocol on the IP-Star® is using the standard &ld...
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    iDeal Library Preparation kit - IP-Star® compact
    The “iDeal Library Preparation” protocol on the IP-Star® is using the standard &l...
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    MicroPlex Library Preparation kit™ v2 - IP-Star Compact
    The “MicroPlex Library Preparation” protocol on the IP-Star® is using the standar...
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    NEBNext® ChIP-Seq Library Prep for Illumina - IP-Star® Compact -
    The “NEBNext_ChIP-Seq_Illumina” protocol on the IP-Star® is using the standard &l...
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    NEBNext® ChIP-Seq Library Prep for Illumina - IP-Star Compact
    The “NEBNext ChIP-Seq Illumina” protocol on the IP-Star® is using the standard &l...
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    TruSeq DNA sample preparation - IP-Star® Compact
    The “TruSeq DNA SamplePrep” protocol on the IP-Star® is using the standard &ldquo...
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    TruSeqTM ChIP Sample Preparation - IP-Star® Compact -
    The “TruSeq ChIP SamplePrep” protocol on the IP-Star® is using the standard &ldqu...
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    TruSeq™ ChIP Sample Preparation - IP-Star® Compact
    The “TruSeq ChIP SamplePrep” protocol on the IP-Star® is using the standard &ldqu...
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    TruSeq™ DNA PCR-Free Sample Preparation - IP-Star Compact
    The “TruSeq™ DNA PCR-Free SamplePrep” protocol on the IP-Star® is using the...
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    TruSeq™ RNA Sample Preparation - IP-Star Compact
    The “TruSeq RNA SamplePrep” protocol on the IP-Star® is using the standard &ldquo...
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    TruSeq™ Stranded RNA Sample Preparation - IP-Star® Compact
    The “TruSeq Stranded RNA SamplePrep” protocol on the IP-Star® is using the standa...
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  • Applications
    Epigenetics Chromatin Analysis
    Epigenetic research addresses the alterations to the chromatin template that collectively establishes and propagates different patterns of transcription or gene expression and silencing from the same genome. The major components of chromatin are... Read more
    Epigenetics DNA Methylation
    Complete solutions for DNA methylation studies Whether you are experienced or new to the field of DNA methylation, Diagenode has everything you need to make your assay as easy and convenient as possible while ensuring consistent data betwee... Read more
    Next Generation Sequencing
    DNA Shearing, library preparation, and automation: your one-stop shop for NGS 1. Choose your shearing device: Shear DNA anywhere from 150 kb to 75 kb Shear down to 5 μl: 150 bp - 2 kb Perfect for NGS DNA libr... Read more
    Methylbinding domain protein
    The MBD approach is based on the very high affinity of a H6-GST-MBD fusion protein for methylated DNA. This protein consists of the methyl binding domain (MBD) of human MeCP2, as a C-terminal fusion with Glutathione-S-transferase (GST) containin... Read more
    Methylated DNA immunoprecipitation
    The Methylated DNA IP (MeDIP) is based on the affinity purification of methylated DNA using an antibody directed against 5-methylcytosine (5-mC) or 5-hydroxymethylcytosine (5-hmC) in the case of hMeDIP. How it works In brief, Methyl DNA IP is ... Read more
    Bisulfite conversion
    Bisulfite modification of DNA is the most commonly used, "gold standard" method for DNA methylation studies providing single nucleotide resolution. This technology is based on the chemical conversion of unmethylated cytosine to uracil. Methylate... Read more
    Library preparation
    Most of the major next-generation sequencing platforms require ligation of specific adaptor oligos to fragmented DNA or RNA prior to sequencing After input DNA has been fragmented, it is end-repaired and blunt-ended. The next step is a A-tail... Read more
    ChIP-seq
    Chromatin Immunoprecipitation (ChIP) coupled with high-throughput massively parallel sequencing as a detection method (ChIP-seq) has become one of the primary methods for epigenomic researches, namely to investigate protein-DNA interaction on a ... Read more
    ChIP-qPCR
    Chromatin Immunoprecipitation (ChIP) coupled with quantitative PCR can be used to investigate protein-DNA interaction at known genomic binding sites. if sites are not known, qPCR primers can also be designed against potential regulatory region... Read more
  • Documents
    Antibody ChIPSeq QC using the IPStar Compact POSTER
    Chromatin immunoprecipitation (ChIP) is the most widely used method to study protein-DNA interact...
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    Automated Solutions for Epigenetics BROCHURE
    SX-8G IP-Star® Compact Automated System High resolution ChIP-seq and MeDIP-seq p...
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    High Resolution ChIPSeq Profiles with IPStar Automated Platform POSTER
    Chromatin immunoprecipitation followed by next generation sequencing (ChIP-Seq) is a powerful tec...
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    Automated method for RNAseq libraries APPLICATION NOTE
    An automated method for efficient, accurate and reproducible construction of RNA-seq libraries
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    Transcription Factor Binding Studies with IP-Star® Compact Automated System CASE STUDY
    High sensitivity automated ChIP experiments to study the transcriptional regulation of th...
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    Automated ChIP with IPStar APPLICATION NOTE
    Screening histone modifications in genomic regions using chromatin from 1,000 to 1 millio...
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    Automated NGS Library Prep with the IP-Star® Compact BROCHURE
    Automated Library Preparation Quick and easy set up, 15 minutes hands-on time Compat...
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    SX-8G IP-Star® Compact MANUAL
    The Diagenode System SX-8G IP-Star® Compact has been developed for the automation of di...
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    True MicroChIP and MicroPlex kits APPLICATION NOTE
    From minuscule amounts to magnificent results: reliable ChIP-seq data from 10,000 cells with the ...
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    Automating Whole-Genome DNA Methylation Analyses POSTER
    A step toward identifying subtle epigenetic variation in cancer and other complex disease
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  • Publications

    How to properly cite this product in your work

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    Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells
    Chen L. et al.
    Characterizing the multifaceted contribution of genetic and epigenetic factors to disease phenotypes is a major challenge in human genetics and medicine. We carried out high-resolution genetic, epigenetic, and transcriptomic profiling in three major human immune cell types (CD14+ monocytes, CD16+ neutrophils, ...

    RNA polymerase II promoter-proximal pausing in mammalian long non-coding genes
    Bunch H et al.
    Mammalian genomes encode a large number of non-coding RNAs (ncRNAs) that greatly exceed mRNA genes. While the physiological and pathological roles of ncRNAs have been increasingly understood, the mechanisms of regulation of ncRNA expression are less clear. Here, our genomic study has shown that a significant number ...

    Epigenetic dynamics of monocyte-to-macrophage differentiation
    Wallner S et al.
    BACKGROUND: Monocyte-to-macrophage differentiation involves major biochemical and structural changes. In order to elucidate the role of gene regulatory changes during this process, we used high-throughput sequencing to analyze the complete transcriptome and epigenome of human monocytes that were differentiated in...

    Genome-wide DNA methylation profiling with MeDIP-seq using archived dried blood spots
    Nicklas H. Staunstrup et al.
    Background In utero and early-life experienced environmental exposures are suggested to play an important role in many multifactorial diseases potentially mediated through lasting effects on the epigenome. As the epigenome in addition remains modifiable throughout life, identifying specific disease-relevant biomarke...

    H3K4 acetylation, H3K9 acetylation and H3K27 methylation in breast tumor molecular subtypes
    Judes G et al.
    AIM: Here, we investigated how the St Gallen breast molecular subtypes displayed distinct histone H3 profiles. PATIENTS & METHODS: 192 breast tumors divided into five St Gallen molecular subtypes (luminal A, luminal B HER2-, luminal B HER2+, HER2+ and basal-like) were evaluated for their histone H3 modifica...

    Characterization of the replication timing program of 6 human model cell lines
    Hadjadj D et al.
    During the S-phase, the DNA replication process is finely orchestrated and regulated by two programs: the spatial program that determines where replication will start in the genome (Cadoret et al. (2008 Oct 14), Cayrou et al. (2011 Sep), Picard et al. (2014 May 1) [1], [2], [3]), and the temporal program that determ...

    H4K5 histone acetylation of BRG1 is associated with heroin administration rather than addiction
    Xu L et al.
    Diacetylmorphine hydrochloride (heroin) addiction is a chronic relapsing brain disorder that is a heavy public health burden worldwide. Brm/SWI2-related gene-1 (BRG1) is a tumor suppressor gene that can influence embryogenesis and the development of the cerebellum. The current study aimed to investigate the effect o...

    Regulation of the DNA Methylation Landscape in Human Somatic Cell Reprogramming by the miR-29 Family
    Hysolli E et al.
    Reprogramming to pluripotency after overexpression of OCT4, SOX2, KLF4, and MYC is accompanied by global genomic and epigenomic changes. Histone modification and DNA methylation states in induced pluripotent stem cells (iPSCs) have been shown to be highly similar to embryonic stem cells (ESCs). However, epigenetic d...

    Epigenetic Modifications with DZNep, NaBu and SAHA in Luminal and Mesenchymal-like Breast Cancer Subtype Cells
    Dagdemir A et al.
    BACKGROUND/AIM: Numerous studies have shown that breast cancer and epigenetic mechanisms have a very powerful interactive relation. The MCF7 cell line, representative of luminal subtype and the MDA-MB 231 cell line representative of mesenchymal-like subtype were treated respectively with a Histone Methyl Transferas...

    Molecular and Epigenetic Biomarkers in Luminal Androgen Receptor: A Triple Negative Breast Cancer Subtype
    Judes G et al.

    Aberrant DNA methylation of WNT pathway genes in the development and progression of CIMP-negative colorectal cancer.
    Galamb O et al.
    The WNT signaling pathway has an essential role in colorectal carcinogenesis and progression, which involves a cascade of genetic and epigenetic changes. We aimed to analyze DNA methylation affecting the WNT pathway genes in colorectal carcinogenesis in promoter and gene body regions using whole methylome analysis i...

    Genome-wide non-CpG methylation of the host genome during M. tuberculosis infection
    Sharma G et al.
    A mammalian cell utilizes DNA methylation to modulate gene expression in response to environmental changes during development and differentiation. Aberrant DNA methylation changes as a correlate to diseased states like cancer, neurodegenerative conditions and cardiovascular diseases have been documented. Here we sho...

    Epigenetic regulation of diacylglycerol kinase alpha promotes radiation-induced fibrosis
    Weigel C. et al.
    Radiotherapy is a fundamental part of cancer treatment but its use is limited by the onset of late adverse effects in the normal tissue, especially radiation-induced fibrosis. Since the molecular causes for fibrosis are largely unknown, we analyse if epigenetic regulation might explain inter-individual differences i...

    Epigenetic profiling in CD4+ and CD8+ T cells from Graves' disease patients reveals changes in genes associated with T cell receptor signaling
    Limbach M, Saare M, Tserel L, Kisand K, Eglit T, Sauer S, Axelsson T, Syvänen AC, Metspalu A, Milani L, Peterson P
    In Graves' disease (GD), a combination of genetic, epigenetic and environmental factors causes an autoimmune response to the thyroid gland, characterized by lymphocytic infiltrations and autoantibodies targeting the thyroid stimulating hormone receptor (TSHR) and other thyroid antigens. To identify the epigenetic ch...

    The Nuclear Ribonucleoprotein SmD1 Interplays with Splicing, RNA Quality Control, and Posttranscriptional Gene Silencing in Arabidopsis
    Elvira-Matelot E. et al.
    RNA quality control (RQC) eliminates aberrant RNAs based on their atypical structure, whereas posttranscriptional gene silencing (PTGS) eliminates both aberrant and functional RNAs through the sequence-specific action of short interfering RNAs (siRNAs). The Arabidopsis thaliana mutant smd1b was identified in a genet...

    DNMT3L enables accumulation and inheritance of epimutations in transgenic Drosophila
    Basu A et al.
    DNMT3L is an important epigenetic regulator in mammals, integrating DNA methylation and histone modification based epigenetic circuits. Here we show DNMT3L to be a part of the machinery that enables inheritance of epigenetic modifications from one generation to the next. Ectopic expression of DNMT3L in Drosophila, w...

    The chloroplastic DEVH-box RNA helicase INCREASED SIZE EXCLUSION LIMIT 2 involved in plasmodesmata regulation is required for group II intron splicing
    Carlotto N, Wirth S, Furman N, Ferreyra Solari N, Ariel F, Crespi M, Kobayashi K
    INCREASED SIZE EXCLUSION LIMIT 2 (ISE2) encodes a putative DEVH-box RNA helicase originally identified through a genetic screening for Arabidopsis mutants altered in plasmodesmata (PD) aperture. Depletion of ISE2 also affects chloroplasts activity, decreases accumulation of photosynthetic pigments and alters express...

    Standardizing chromatin research: a simple and universal method for ChIP-seq
    Laura Arrigoni, Andreas S. Richter, Emily Betancourt, Kerstin Bruder, Sarah Diehl, Thomas Manke and Ulrike Bönisch
    Here we demonstrate that harmonization of ChIP-seq workflows across cell types and conditions is possible when obtaining chromatin from properly isolated nuclei. We established an ultrasound-based nuclei extraction method (Nuclei Extraction by Sonication) that is highly effective across various organisms, cell ...

    A highly conserved NF-κB-responsive enhancer is critical for thymic expression of Aire in mice
    Haljasorg U et al.
    Autoimmune regulator (Aire) has a unique expression pattern in thymic medullary epithelial cells (mTECs), in which it plays a critical role in the activation of tissue-specific antigens. The expression of Aire in mTECs is activated by receptor activator of nuclear factor κB (RANK) signaling; however, the molec...

    Progressive Chromatin Condensation and H3K9 Methylation Regulate the Differentiation of Embryonic and Hematopoietic Stem Cells
    Ugarte F at al.
    Epigenetic regulation serves as the basis for stem cell differentiation into distinct cell types, but it is unclear how global epigenetic changes are regulated during this process. Here, we tested the hypothesis that global chromatin organization affects the lineage potential of stem cells and that manipulation of c...

    Loss of BAP1 function leads to EZH2-dependent transformation
    LaFave ML et al.
    The tumor suppressors BAP1 and ASXL1 interact to form a polycomb deubiquitinase complex that removes monoubiquitin from histone H2A lysine 119 (H2AK119Ub). However, BAP1 and ASXL1 are mutated in distinct cancer types, consistent with independent roles in regulating epigenetic state and malignant transformation. Here...

    Transcription Factor Repertoire of Homeostatic Eosinophilopoiesis
    Bouffi C, Kartashov AV, Schollaert KL, Chen X, Bacon WC, Weirauch MT, Barski A, Fulkerson PC
    The production of mature eosinophils (Eos) is a tightly orchestrated process with the aim to sustain normal Eos levels in tissues while also maintaining low numbers of these complex and sensitive cells in the blood. To identify regulators of homeostatic eosinophilopoiesis in mice, we took a global approach to identi...

    Comparative analysis of anti-viral transcriptomics reveals novel effects of influenza immune antagonism
    Thakar J, Hartmann BM, Marjanovic N, Sealfon SC, Kleinstein SH
    BACKGROUND: Comparative analysis of genome-wide expression profiles are increasingly being used to study virus-specific host interactions. In order to gain mechanistic insights, gene expression profiles can be combined with information on DNA-binding sites of transcription factors to detect transcription factor a...

    The interaction of mycobacterial protein Rv2966c with host chromatin is mediated through non-CpG methylation and histone H3/H4 binding.
    Sharma G, Upadhyay S, Srilalitha M, Nandicoori VK, Khosla S
    To effectively modulate the gene expression within an infected mammalian cell, the pathogen Mycobacterium tuberculosis would need to bring about epigenetic modifications at appropriate genomic loci. Working on this hypothesis, we show in this study that the mycobacterial protein Rv2966c is a 5-methylcytosine-specifi...

    An automated method for efficient, accurate and reproducible construction of RNA-seq libraries.
    Tsompana M, Valiyaparambil S, Bard J, Marzullo B, Nowak N, Buck MJ
    BACKGROUND: Integration of RNA-seq expression data with knowledge on chromatin accessibility, histone modifications, DNA methylation, and transcription factor binding has been instrumental for the unveiling of cell-specific local and long-range regulatory patterns, facilitating further investigation on the underlyin...

    Bacterial Infection Remodels the DNA Methylation Landscape of Human Dendritic Cells
    Pacis A, Tailleux L, Lambourne J, Yotova V, Dumaine A, Danckaert A, Luca F, Grenier JC, Hansen K, Gicquel B, Yu M, Pai A, Tung J, He C, Pastinen T, Pique-Regi R, Gilad Y, Barreiro L
    DNA methylation is thought to be robust to environmental perturbations on a short time scale. Here, we challenge that view by demonstrating that the infection of human dendritic cells (DCs) with a pathogenic bacteria is associated with rapid changes in methylation at thousands of loci. Infection-induced changes in m...

    The histone demethylase enzyme KDM3A is a key estrogen receptor regulator in breast cancer.
    Wade MA, Jones D, Wilson L, Stockley J, Coffey K, Robson CN, Gaughan L
    Endocrine therapy has successfully been used to treat estrogen receptor (ER)-positive breast cancer, but this invariably fails with cancers becoming refractory to treatment. Emerging evidence has suggested that fluctuations in ER co-regulatory protein expression may facilitate resistance to therapy and be involved i...

    A Novel Role for Kruppel-like Factor 14 (KLF14) in T-Regulatory Cell Differentiation
    Sarmento OF, Svingen PA, Xiong Y, Xavier RJ, McGovern D, Smyrk TC, Papadakis K, Urrutia RA, Faubion WA
    Background & Aims Kruppel-like Factor 14 (KLF14) proteins function as epigenetic reprogramming factors during cell differentiation in many cell populations and in engineered induced pluripotent stem cells. In this study, we determined the function of KLF14 in the regulation of forkhead box protein 3 (FOXP3), a t...

    Polycomb Repressive Complex 2 Regulates Lineage Fidelity during Embryonic Stem Cell Differentiation.
    Thornton SR, Butty VL, Levine SS, Boyer LA
    Polycomb Repressive Complex 2 (PRC2) catalyzes histone H3 lysine 27 tri-methylation (H3K27me3), an epigenetic modification associated with gene repression. H3K27me3 is enriched at the promoters of a large cohort of developmental genes in embryonic stem cells (ESCs). Loss of H3K27me3 leads to a failure of ESCs to pro...

    Automating ChIP-seq Experiments to Generate Epigenetic Profiles on 10,000 HeLa Cells.
    Berguet G, Hendrickx J, Sabatel C, Laczik M, Squazzo S, Mazon Pelaez I, Saxena R, Pendeville H, Poncelet D
    Chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) is a technique of choice for studying protein-DNA interactions. ChIP-seq has been used for mapping protein-DNA interactions and allocating histones modifications. The procedure is tedious and time consuming, and one of the major limitati...

    Long noncoding RNA modulates alternative splicing regulators in Arabidopsis.
    Bardou F, Ariel F, Simpson CG, Romero-Barrios N, Laporte P, Balzergue S, Brown JW, Crespi M
    Alternative splicing (AS) of pre-mRNA represents a major mechanism underlying increased transcriptome and proteome complexity. Here, we show that the nuclear speckle RNA-binding protein (NSR) and the AS competitor long noncoding RNA (or ASCO-lncRNA) constitute an AS regulatory module. AtNSR-GFP translational fusions...

    Genome-wide association analysis of eosinophilic esophagitis provides insight into the tissue specificity of this allergic disease.
    Kottyan LC, Davis BP, Sherrill JD, Liu K, Rochman M, Kaufman K, Weirauch MT, Vaughn S, Lazaro S, Rupert AM, Kohram M, Stucke EM, Kemme KA, Magnusen A, He H, Dexheimer P, Chehade M, Wood RA, Pesek RD, Vickery BP, Fleischer DM, Lindbad R, Sampson HA, Mukkad
    Eosinophilic esophagitis (EoE) is a chronic inflammatory disorder associated with allergic hypersensitivity to food. We interrogated >1.5 million genetic variants in EoE cases of European ancestry and subsequently in a multi-site cohort with local and out-of-study control subjects. In addition to replicating asso...

    Noncoding Transcription by Alternative RNA Polymerases Dynamically Regulates an Auxin-Driven Chromatin Loop.
    Ariel F, Jegu T, Latrasse D, Romero-Barrios N, Christ A, Benhamed M, Crespi M
    The eukaryotic epigenome is shaped by the genome topology in three-dimensional space. Dynamic reversible variations in this epigenome structure directly influence the transcriptional responses to developmental cues. Here, we show that the Arabidopsis long intergenic noncoding RNA (lincRNA) APOLO is transcribed by RN...

    Two CCAAT box-binding transcription factors redundantly regulate early steps of the legume-rhizobia endosymbiosis.
    Laloum T, Baudin M, Frances L, Lepage A, Billault-Penneteau B, Cerri MR, Ariel F, Jardinaud MF, Gamas P, de Carvalho-Niebel F, Niebel A
    During endosymbiotic interactions between legume plants and nitrogen-fixing rhizobia, successful root infection by bacteria and nodule organogenesis requires the perception and transduction of bacterial lipo-chitooligosaccharidic signal called Nod Factor (NF). NF perception in legume roots leads to the activation of...

    Early aberrant DNA methylation events in a mouse model of acute myeloid leukemia.
    Sonnet M, Claus R, Becker N, Zucknick M, Petersen J, Lipka DB, Oakes CC, Andrulis M, Lier A, Milsom MD, Witte T, Gu L, Kim-Wanner SZ, Schirmacher P, Wulfert M, Gattermann N, Lübbert M, Rosenbauer F, Rehli M, Bullinger L, Weichenhan D, Plass C
    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 leukemic progression are largely unknown. METHODS: We screened genome-wide fo...

    Stable methylation at promoters distinguishes Epiblast Stem Cells from Embryonic Stem Cells and the in vivo epiblast.
    Veillard AC, Marks H, Bernardo AS, Jouneau L, Laloe D, Boulanger L, Kaan A, Brochard V, Tosolini M, Pedersen R, Stunnenberg H, Jouneau A.
    Embryonic Stem Cells (ESCs) and Epiblast Stem Cells (EpiSCs) are the in vitro representatives of naïve and primed pluripotency, respectively. It is currently unclear how their epigenomes underpin the phenotypic and molecular characteristics of these distinct pluripotent states. Here, we performed a genome-wide ...

    MBD4 cooperates with DNMT1 to mediate methyl-DNA repression and protects mammalian cells from oxidative stress.
    Laget S, Miotto B, Chin HG, Estève PO, Roberts RJ, Pradhan S, Defossez PA
    Oxidative stress induces genome-wide remodeling of the chromatin structure. In this study, we identify Methyl-CpG Binding Protein 4 (MBD4), a multifunctional enzyme involved in DNA demethylation, base excision repair, and gene expression regulation, as an essential factor in response to oxidative stress. We provide ...

    Human-specific epigenetic variation in the immunological Leukotriene B4 Receptor (LTB4R/BLT1) implicated in common inflammatory diseases.
    Wilson GA, Butcher LM, Foster HR, Feber A, Roos C, Walter L, Woszczek G, Beck S, Bell CG
    BACKGROUND: Common human diseases are caused by the complex interplay of genetic susceptibility as well as environmental factors. Due to the environment's influence on the epigenome, and therefore genome function, as well as conversely the genome's facilitative effect on the epigenome, analysis of this level of regu...

    Demethylation of the human eotaxin-3 gene promoter leads to the elevated expression of eotaxin-3.
    Lim E, Rothenberg ME
    DNA demethylation has been primarily studied in the context of development biology, cell fate, and cancer, with less attention on inflammation. In this article, we investigate the association between DNA methylation and production of the chemoattractant cytokine eotaxin-3 in the tissue of patients with allergic dise...

    Differential methylation of the TRPA1 promoter in pain sensitivity.
    Bell JT, Loomis AK, Butcher LM, Gao F, Zhang B, Hyde CL, Sun J, Wu H, Ward K, Harris J, Scollen S, Davies MN, Schalkwyk LC, Mill J, , Williams FM, Li N, Deloukas P, Beck S, McMahon SB, Wang J, John SL, Spector TD
    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 unrelated individuals. Whole-blood DNA methylation was characterized a...

    Toxoplasma gondii inhibits IFN-γ- and IFN-β-induced host cell STAT1 transcriptional activity by increasing the association of STAT1 with DNA.
    Rosowski EE, Nguyen QP, Camejo A, Spooner E, Saeij JP
    The IFN-γ response, mediated by the STAT1 transcription factor, is crucial for host defense against the intracellular pathogen Toxoplasma gondii, but prior infection with Toxoplasma can inhibit this response. Recently it was reported that the Toxoplasma type II NTE strain prevents the recruitment of chromatin ...

    Reactive Oxygen Species Induce Epigenetic Instability through the Formation of 8-Hydroxydeoxyguanosine in Human Hepatocarcinogenesis.
    Nishida N, Arizumi T, Takita M, Kitai S, Yada N, Hagiwara S, Inoue T, Minami Y, Ueshima K, Sakurai T, Kudo M
    Chronic hepatitis C (CHC) triggers oxidative stress and contributes to the emergence of hepatocellular carcinoma (HCC). We previously reported that tumor suppressor gene (TSG) methylation is a critical factor during the early stages of hepatocarcinogenesis. In this study, we clarify the association between oxidative...

    Lack of decorin expression by human bladder cancer cells offers new tools in the therapy of urothelial malignancies.
    Sainio A, Nyman M, Lund R, Vuorikoski S, Boström P, Laato M, Boström PJ, Järveläinen H
    Decorin, a multifunctional small leucine-rich extracellular matrix proteoglycan, has been shown to possess potent antitumour activity. However, there is some uncertainty whether different cancer cells express decorin in addition to non-malignant stromal cells. In this study we clarified decorin expression by human b...

    DNA methylation analysis of murine hematopoietic side population cells during aging.
    Taiwo O, Wilson GA, Emmett W, Morris T, Bonnet D, Schuster E, Adejumo T, Beck S, Pearce DJ.
    Stem cells have been found in most tissues/organs. These somatic stem cells produce replacements for lost and damaged cells, and it is not completely understood how this regenerative capacity becomes diminished during aging. To study the possible involvement of epigenetic changes in somatic stem cell aging, we used ...

    Global alterations of DNA methylation in cholangiocarcinoma targets the Wnt signaling pathway
    Goeppert B, Konermann C, Schmidt CR, Bogatyrova O, Geiselhart L, Ernst C, Gu L, Becker N, Zucknick M, Mehrabi A, Hafezi M, Klauschen F, Stenzinger A, Warth A, Breuhahn K, Renner M, Weichert W, Schirmacher P, Plass C, Weichenhan D
    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 CC, data regarding global methylation changes are lacking so far. We p...

    Integrated virus-host methylome analysis in head and neck squamous cell carcinoma
    Wilson GA, Lechner M, Köferle A, Caren H, Butcher LM, Feber A, Fenton T, Jay A, Boshoff C, Beck S
    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 DNA methylation analysis using MeDIP-seq of HPV+ and HPV- head and neck ...

    Meta-analysis of IDH-mutant cancers identifies EBF1 as an interaction partner for TET2.
    Guilhamon P, Eskandarpour M, Halai D, Wilson GA, Feber A, Teschendorff AE, Gomez V, Hergovich A, Tirabosco R, Fernanda Amary M, Baumhoer D, Jundt G, Ross MT, Flanagan AM, Beck S
    Isocitrate dehydrogenase (IDH) genes 1 and 2 are frequently mutated in acute myeloid leukaemia (AML), low-grade glioma, cholangiocarcinoma (CC) and chondrosarcoma (CS). For AML, low-grade glioma and CC, mutant IDH status is associated with a DNA hypermethylation phenotype, implicating altered epigenome dynamics in t...

    HPV-related methylation signature predicts survival in oropharyngeal squamous cell carcinomas.
    Kostareli E, Holzinger D, Bogatyrova O, Hielscher T, Wichmann G, Keck M, Lahrmann B, Grabe N, Flechtenmacher C, Schmidt CR, Seiwert T, Dyckhoff G, Dietz A, Höfler D, Pawlita M, Benner A, Bosch FX, Plinkert P, Plass C, Weichenhan D, Hess J
    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 compared with HPV-negative patients, but the underlying molecular mechanisms ...

    SOX2 co-occupies distal enhancer elements with distinct POU factors in ESCs and NPCs to specify cell state.
    Lodato MA, Ng CW, Wamstad JA, Cheng AW, Thai KK, Fraenkel E, Jaenisch R, Boyer LA
    SOX2 is a master regulator of both pluripotent embryonic stem cells (ESCs) and multipotent neural progenitor cells (NPCs); however, we currently lack a detailed understanding of how SOX2 controls these distinct stem cell populations. Here we show by genome-wide analysis that, while SOX2 bound to a distinct set of ge...

    Identification and functional validation of HPV-mediated hypermethylation in head and neck squamous cell carcinoma.
    Lechner M, Fenton T, West J, Wilson G, Feber A, Henderson S, Thirlwell C, Dibra HK, Jay A, Butcher L, Chakravarthy AR, Gratrix F, Patel N, Vaz F, O'Flynn P, Kalavrezos N, Teschendorff AE, Boshoff C, Beck S
    BACKGROUND: Human papillomavirus-positive (HPV+) head and neck squamous cell carcinoma (HNSCC) represents a distinct clinical and epidemiological condition compared with HPV-negative (HPV-) HNSCC. To test the possible involvement of epigenetic modulation by HPV in HNSCC, we conducted a genome-wide DNA-methylation an...

    Linking proteomic and transcriptional data through the interactome and epigenome reveals a map of oncogene-induced signaling.
    Huang SS, Clarke DC, Gosline SJ, Labadorf A, Chouinard CR, Gordon W, Lauffenburger DA, Fraenkel E
    Cellular signal transduction generally involves cascades of post-translational protein modifications that rapidly catalyze changes in protein-DNA interactions and gene expression. High-throughput measurements are improving our ability to study each of these stages individually, but do not capture the connections bet...

    Histone lysine trimethylation or acetylation can be modulated by phytoestrogen, estrogen or anti-HDAC in breast cancer cell lines.
    Dagdemir A, Durif J, Ngollo M, Bignon YJ, Bernard-Gallon D
    AIM: The isoflavones genistein, daidzein and equol (daidzein metabolite) have been reported to interact with epigenetic modifications, specifically hypermethylation of tumor suppressor genes. The objective of this study was to analyze and understand the mechanisms by which phytoestrogens act on chromatin in breast c...

    Nano-MeDIP-seq: Methylome analysis using low DNA concentrations (Prot 58)
    Taiwo O, Wilsona GA, Morris T, Seisenberger S, Reik W, Pearce D, Beck S, Butcher LM
    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 input to minimise the drain on precious samples. MeDIP-seq fulfils thes...

    Comparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues
    Simmer F, Brinkman AB, Assenov Y, Matarese F, Kaan A, Sabatino L, Villanueva A, Huertas D, Esteller M, Lengauer T, Bock C, Colantuoni V, Altucci L, Stunnenberg HG.
    Aberrant DNA methylation often occurs in colorectal cancer (CRC). In our study we applied a genome-wide DNA methylation analysis approach, MethylCap-seq, to map the differentially methylated regions (DMRs) in 24 tumors and matched normal colon samples. In total, 2687 frequently hypermethylated and 468 frequently hyp...

    HMGA1 Reprograms Somatic Cells into Pluripotent Stem Cells by Inducing Stem Cell Transcriptional Networks.
    Shah SN, Kerr C, Cope L, Zambidis E, Liu C, Hillion J, Belton A, Huso DL, Resar LM
    BACKGROUND: Although recent studies have identified genes expressed in human embryonic stem cells (hESCs) that induce pluripotency, the molecular underpinnings of normal stem cell function remain poorly understood. The high mobility group A1 (HMGA1) gene is highly expressed in hESCs and poorly differentiated, stem-l...

    Human-specific CpG "beacons" identify loci associated with human-specific traits and disease.
    Bell CG, Wilson GA, Butcher LM, Roos C, Walter L, Beck S
    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 variability via DNA methylation, and this epigenetic mark functions as a regulat...

    ERG and FLI1 binding sites demarcate targets for aberrant epigenetic regulation by AML1-ETO in acute myeloid leukemia.
    Martens JH, Mandoli A, Simmer F, Wierenga BJ, Saeed S, Singh AA, Altucci L, Vellenga E, Stunnenberg HG
    ERG and FLI1 are closely related members of the ETS family of transcription factors and have been identified as essential factors for the function and maintenance of normal hematopoietic stem cells. Here, genome-wide analysis revealed that both ERG and FLI1 occupy similar genomic regions as AML1-ETO in t(8;21) AMLs ...

    Extensive promoter hypermethylation and hypomethylation is associated with aberrant microRNA expression in chronic lymphocytic leukemia.
    Baer C, Claus R, Frenzel LP, Zucknick M, Park YJ, Gu L, Weichenhan D, Fischer M, Pallasch CP, Herpel E, Rehli M, Byrd JC, Wendtner CM, Plass C
    Dysregulated microRNA (miRNA) expression contributes to the pathogenesis of hematopoietic malignancies, including chronic lymphocytic leukemia (CLL). However, an understanding of the mechanisms that cause aberrant miRNA transcriptional control is lacking. In this study, we comprehensively investigated the role and e...

    High throughput automated chromatin immunoprecipitation as a platform for drug screening and antibody validation.
    Wu AR, Kawahara TL, Rapicavoli NA, Riggelen JV, Shroff EH, Xu L, Felsher DW, Chang HY, Quake SR
    Chromatin immunoprecipitation (ChIP) is an assay for interrogating protein-DNA interactions that is increasingly being used for drug target discovery and screening applications. Currently the complexity of the protocol and the amount of hands-on time required for this assay limits its use to low throughput applicati...

    Methylome analysis using MeDIP-seq with low DNA concentrations.
    Taiwo O, Wilson GA, Morris T, Seisenberger S, Reik W, Pearce D, Beck S, Butcher LM
    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 technique that balances accuracy, genome coverage, resolution and cost,...

    Quality control and single nucleotide resolution analysis of methylated DNA immunoprecipitation products.
    Sengenès J, Daunay A, Charles MA, Tost J
    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 to assess the quality and the detailed methylation patterns of the immu...

    Whole-genome DNA methylation profiling using MethylCap-seq.
    Brinkman AB, Simmer F, Ma K, Kaan A, Zhu J, Stunnenberg HG
    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 captured methylated DNA is done in steps using a salt gradient, which stratif...

    AutoMeDIP-seq: A high-throughput, whole genome, DNA methylation assay
    Butcher LM, Beck S
    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-throughput and agnostic with respect to genomic features. To this end, the...

    A highly conserved NF-κB-responsive enhancer is critical for thymic expression of Aire in mice
    Haljasorg U, Bichele R, Saare M, Guha M, Maslovskaja J, Kõnd K, Remm A, Pihlap M, Tomson L, Kisand K, Laan M, Peterson P
    Autoimmune regulator (AIRE) has a unique expression pattern in thymic medullary epithelial cells (mTECs), in which it plays a critical role in the activation of tissue-specific antigens. The expression of Aire in mTECs is activated by RANK signaling; however, the molecular mechanism behind this activation is unknown...

    Using ChIP-Seq Technology to Generate High-Resolution Profiles of Histone Modifications
    O’Geen H, Echipare L, Farnham PJ
    The dynamic modification of DNA and histones plays a key role in transcriptional regulation through - altering the packaging of DNA and modifying the nucleosome surface. These chromatin states, also referred to as the epigenome, are distinctive for different tissues, developmental stages, and disease states and can ...

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