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Series GSE30203 Query DataSets for GSE30203
Status Public on Dec 09, 2011
Title DNA binding factors shape the mouse methylome at distal regulatory regions [ChIP-seq].
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary To gain insights into the interplay between DNA methylation and gene regulation we generated a basepair resolution reference map of the mouse methylome in stem cells and neurons. High genome coverage allowed for a novel quantitative analysis of local methylation states, which identified Low Methylated Regions (LMR) with an average methylation of 30%. These regions are evolutionary conserved, reside outside of CpG islands and distal to promoters. They represent regulatory regions evidenced by their DNaseI hypersensitivity and chromatin marks of enhancer elements. LMRs are occupied by transcription factors (TF) and their reduced methylation requires TF binding while introduction of TF binding sites creates LMRs de novo. This dependency on TF activity is further evident when comparing the methylomes of embryonic stem cells and derived neuronal cells. LMRs present in both cell types are occupied by broadly expressed factors, while LMRs present at only one state are occupied by cell-type specific TFs. Methylome data can thus enhance the prediction of occupied TF binding sites and identification of active regulatory regions genome-wide. Our study provides reference methylomes for the mouse at two cell states, identifies a novel and highly dynamic feature of the epigenome that defines distal regulatory elements and shows that transcription factor binding dynamically shapes mammalian methylomes.
Overall design Whole genome shotgun bisulfite sequencing of mouse embryonic stem (ES) cells and derived neuronal progenitors (NP). CTCF ChIP sequencing in mouse ES and Dnmt1/3a/3b triple knock-out ES (TKO) cells. H3K4me1, H3K4me2 and H3K27me3 ChIP sequencing in mouse ES cells. Pax6 ChIP-chip in mouse ES cells.
Contributor(s) Stadler MB, Murr R, Burger L, Ivanek R, Lienert F, Scholer A, Oakeley EJ, Gaidatzis D, Tiwari V, Schubeler D
Citation(s) 22170606
Submission date Jun 24, 2011
Last update date May 15, 2019
Contact name Dirk Schuebeler
Organization name Friedrich Miescher Institute for Biomedical Research
Street address Maulbeerstrasse 66
City Basel
ZIP/Postal code 4058
Country Switzerland
Platforms (1)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
Samples (16)
GSM747534 ES_CTCF_ChIPseq_rep1
GSM747535 ES_CTCF_ChIPseq_rep2
GSM747536 ES_CTCF_ChIPseq_rep3
This SubSeries is part of SuperSeries:
GSE30206 DNA binding factors shape the mouse methylome at distal regulatory regions.
SRA SRP007352
BioProject PRJNA155095

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE30203_RAW.tar 236.1 Mb (http)(custom) TAR (of WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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