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Series GSE41472 Query DataSets for GSE41472
Status Public on Feb 11, 2014
Title Epigenetic regulation of gene expression is instructed by promoter sequence and refined by developmental progression
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary A large body of literature suggests that local features of chromatin are crucial in determining functional properties of underlying DNA. The extent to which DNA sequence plays an active role in the establishment and maintenance of patterns of histone and DNA modification at promoters in cells and tissues in an adult animal remains poorly understood. Likewise, whether passage through development is required for refinement of transcriptional states and chromatin marks characteristic of fully differentiated adult cells remains unclear. Here we undertook analysis of gene expression along with the genomic distribution of DNA methylation and a set of histone marks in primary tissues derived from different primordial germ layers in adult mice. We find that promoter CpG content correlated strongly with specific repressive mechanisms. Likewise, RNA polymerase II occupancy and active histone marks were omnipresent on CpG rich promoters regardless of transcriptional output and of cell type. However, these same chromatin features cleanly demarcate transcriptional activity on promoters with low CpG content. While these observations imply an instructive role for DNA sequence in establishment and maintenance of epigenetic states, experimental evidence presented here also suggests an additional role for development in refining these features at individual promoters.
Overall design Examination of H3K36me3, S5ph pol2, and S2ph pol2 in liver using ChIP-seq.
Contributor(s) Li R, Wade PA, Grimm S
Citation(s) 24521667
Submission date Oct 10, 2012
Last update date May 15, 2019
Contact name ruifang li
Organization name NIEHS
Street address 111 T.W. Alexander Drive
City RTP
State/province NC
ZIP/Postal code 27709
Country USA
Platforms (1)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
Samples (7)
GSM1017928 H3K36me3_ChIPSeq Rep1
GSM1017929 H3K36me3_ChIPSeq Rep2
GSM1017930 S5ph pol2_ChIPSeq Rep1
BioProject PRJNA177165
SRA SRP016061

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Supplementary file Size Download File type/resource
GSE41472_H3K36me3.bedGraph.gz 317.4 Mb (ftp)(http) BEDGRAPH
GSE41472_S2phPol2.bedGraph.gz 142.1 Mb (ftp)(http) BEDGRAPH
GSE41472_S5phPol2.bedGraph.gz 167.8 Mb (ftp)(http) BEDGRAPH
GSE41472_input.bedGraph.gz 89.0 Mb (ftp)(http) BEDGRAPH
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