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H3K27me3 ChIP-seq in DNMT triple knock-out mESCs

ABSTRACT: We immunoprecipitated formaldehyde crosslinked chromatin from DNMT triple knockout cells using an antibody against methylated lysine 27 on histone H3. Subsequent high-throughput sequencing allowed us to study the genome-wide distribution of this histone mark in the absence of DNA methylation.

ORGANISM(S): Mus musculus

PROVIDER: GSE56110 | GEO | 2014/03/22

SECONDARY ACCESSION(S): PRJNA242438

REPOSITORIES: GEO

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H3K27me3 ChIP-seq in DNMT triple knock-out mESCs

Project description:We immunoprecipitated formaldehyde crosslinked chromatin from DNMT triple knockout cells using an antibody against methylated lysine 27 on histone H3. Subsequent high-throughput sequencing allowed us to study the genome-wide distribution of this histone mark in the absence of DNA methylation. Examination of a histone modification in mESCs lacking DNA methylation.

2014-03-22 | E-GEOD-56110 | biostudies-arrayexpress

Differential roles of promoters, enhancers, and insulators in cell-type specific gene expression

Project description:Chromatin immunoprecipitation was performed using antibodies against CTCF and formaldehyde crosslinked chromatin from K562 Chromatin cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions. Keywords: ChIP-chip

2008-11-01 | GSE8098 | GEO

HDAC mediated suppression of histone turnover promotes epigenetic stability of heterochromatin

Project description:Analysis of histone H3 turnover in wild-type and mutant fission yeast cells by using MNase-ChIP-chip Exponentially growing cultures of fission yeast cells expressing an ectopic copy of FLAG tagged histone H3 under the control of inv1 promoter were synchronized and expression of H3-FLAG was induced by changing the carbon source of the medium to Sucrose. Cells were crosslinked with 1% Formaldehyde and chromatin was fragmented into mononucleosomes by using micrococcal nuclease (MNase). Chromatin immunoprecipitated DNA recovered with anti-FLAG antibody from wild-type and mutant fission yeast cells and whole cell extracts DNA were amplified by random priming and respectively labeled with Cy5 and Cy3. Labeled DNA samples were mixed and hybridized onto 44k pombe Agilent oligo arrays. Data were processed using Agilent scanner and Feature Extraction software.

2013-04-21 | E-GEOD-45378 | biostudies-arrayexpress

Differential roles of promoters, enhancers, and insulators in cell-type specific gene expression

2010-05-17 | E-GEOD-8098 | biostudies-arrayexpress

DNMT inhibition in the Neonatal Preoptic Area

Project description:PN2 male and female rat pups were treated with vehicle or zebularine. POA RNA was extracted and sequenced to deterime the effects of DNMT inhibition in POA gene expression. Males and Females were treated with either vehicle (0.1% DNMSO in saline) or Zebularine

2015-03-30 | E-GEOD-66203 | biostudies-arrayexpress

DNA methyltransferase (DNMT) associated proteins in human malaria parasite Plasmodium falciparum

Project description:This study identified Plasmodium falciparum DNA methyltransferase (DNMT)associated proteins in parasite cytosol and nucleus, including RNA binding proteins and AP2-domain containing proteins, indicating this protein is involved in RNA process and transctiptional regulation.

2023-07-20 | PXD032860 | Pride

DNMT inhibition in the Neonatal Preoptic Area

Project description:PN2 male and female rat pups were treated with vehicle or zebularine. POA RNA was extracted and sequenced to deterime the effects of DNMT inhibition in POA gene expression.

2015-03-30 | GSE66203 | GEO

DNA sequence at CpG islands directly influences chromatin structure via the CpG binding protein Cfp1

Project description:CpG islands (CGIs) are prominent in the mammalian genome due to their G+C rich base composition and high density of CpG dinucleotides. Most mammalian gene promoters are embedded within CGIs that lack DNA methylation and coincide with sites of histone H3 lysine 4 trimethylation (H3K4me3),irrespective of transcriptional activity. In spite of these intriguing correlations, the functional significance of non-methylated CGI sequences with respect to chromatin structure and transcription is unknown. High throughput sequencing of Cfp1-bound chromatin identified a striking concordance with non-methylated CGIs and sites of H3K4me3 in the mouse brain. Protocol: Brains were manually homogenised to a single cells suspension and crosslinked using 1% formaldehyde. Chromatin was sheared using a combination of Micrococcal nuclease and sonication (Skene et al, Mol Cell, 2010). Cells were crosslinked using 1% formaldehyde and chromatin sheared using sonication.Protein-DNA complexes were immunoprecipitated with the appropriate antibody and DNA was subsequently extracted. Adaptors were ligated to purified DNA which was then amplified by PCR. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols Sequencing was performed at the Wellcome Trust Sanger Institute; Hinxton, Cambridge, UK.This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

2012-07-18 | E-ERAD-79 | biostudies-arrayexpress

Integration of epigenetic and transcriptional mechanisms governs functional commitment versus plasticity of gd T cell subsets

Project description:gd T cells are major innate sources of interleukin-17 (IL-17) and interferon-g (IFN-g), which are differentially produced by two thymically-derived subsets segregated on CD27 expression. However, the molecular mechanisms that program the functional differentiation of gd cells remain incompletely understood. Here we show that CD27+ gd cells are epigenetically committed to express Ifng but not Il17, whereas CD27- gd cells spontaneously make IL-17 but can be induced to produce IFN-g under specific inflammatory conditions. This M-bM-^@M-^\plasticM-bM-^@M-^] behavior of CD27- gd cells associates with permissive histone H3 marks at loci encoding Ifng and upstream M-bM-^@M-^\type 1M-bM-^@M-^] transcription factors. By contrast, Il17 and related M-bM-^@M-^\type 17M-bM-^@M-^] factors are epigenetically and transcriptionally active in CD27- but silenced in CD27+ gd cells. Hence, stable versus plastic behaviors of gd cell subsets are controlled by integrated epigenetic and transcriptional mechanisms that regulate the expression of M-bM-^@M-^\masterM-bM-^@M-^] transcription factors and effector cytokine genes. ChIP was carried out on FACS-sorted cells from pooled spleen/ lymph nodes. The following antibodies were used: anti-histone H3K4me2 (07-030, Millipore) and anti-histone H3k27me3 (07-449, Millipore). Between 105 - 106 cells were crosslinked with formaldehyde and nuclei were isolated and sonicated with a Sanyo Soniprep 150 at an amplitude of 10 microns with 17 times 10s bursts, resulting in 200M-bM-^@M-^S400bp chromatin fragments. IP was carried out as previously described 49. The Immunoprecipitated DNA released from crosslinked proteins was extracted with the QiaQuick kit (Qiagen) in accordance with the manufacturerM-BM-4s instructions. Deep sequencing was performed at the GeneCore facility of EMBL (http://www.genecore.embl.de/). At least 1 ng of immunoprecipitated DNA was used for library preparation according to the Illumina protocol.

2013-09-01 | E-GEOD-42098 | biostudies-arrayexpress

ChIP-seq of the multiple antibiotic resistance activator (MarA) protein and RNA polymerase sigma70 subunit of Enterotoxigenic Escherichia coli strain H10407

Project description:The experiment contains ChIP-seq data for Enterotoxigenic Escherichia coli strain H10407 transformed with plasmid pRGM9818. The strain was grown at 37 degrees in LB medium and crosslinked with 1 % (v/v) formaldehyde. After sonication, to break open cells and fragment DNA, immunoprecipitations were done using antibodies against MarA, MarR or the RNA polymerase sigma 70 subunit. Libraries were prepared using DNA remaining after immunoprecipitation. Note that the MarR immunoprecipitations were not successful but the data served as a useful control for non-specifically immunoprecipitated DNA sequences.

2017-09-30 | E-MTAB-5521 | biostudies-arrayexpress

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