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Series GSE30641 Query DataSets for GSE30641
Status Public on Mar 16, 2012
Title Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb.
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary The regulatory elements that direct tissue-specific gene expression in the developing mammalian embryo remain largely unknown. Although chromatin profiling has proven to be a powerful method for mapping regulatory sequences in cultured cells, chromatin states characteristic of active developmental enhancers have not been directly identified in embryonic tissues. Here we use whole transcriptome analysis coupled with genome-wide profiling of H3K27ac and H3K27me3 to map chromatin states and enhancers in mouse embryonic forelimb and hindlimb. We show that gene expression differences between forelimb and hindlimb, and between limb and other embryonic cell types, are correlated with tissue-specific H3K27ac signatures at promoters and distal sites. Using H3K27ac profiles, we identified 28,377 putative enhancers, many of which are likely to be limb-specific based on strong enrichment near genes highly expressed in the limb and comparisons with tissue-specific p300 sites and known enhancers. We describe a chromatin state signature associated with active developmental enhancers, defined by high levels of H3K27ac marking, nucleosome displacement, hypersensitivity to sonication, and strong depletion of H3K27me3. We also find that developmental enhancers exhibit components of this signature, including hypersensitivity, H3K27ac enrichment and H3K27me3 depletion, at lower levels in tissues in which they are not active. Our results establish histone modification profiling as a tool for developmental enhancer discovery, and suggest that enhancers maintain an open chromatin state in multiple embryonic tissues independent of their activity level.
Overall design Examination of genome wide H3K27ac and H3K27me3 histone modifications and gene expression in early mouse embryonic limb tissue.
Contributor(s) Cotney J, Noonan J
Citation(s) 22421546
Submission date Jul 13, 2011
Last update date May 15, 2019
Contact name Justin Cotney
Organization name UConn Health
Department Genetics and Genome Sciences
Lab Cotney Lab
Street address 400 Farmington Ave.
City Farmington
State/province CT
ZIP/Postal code 06030-6403
Country USA
Platforms (2)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (24)
GSM759858 E10.5_forelimb_ChIP_input_rep1
GSM759859 E10.5_forelimb_ChIP_input_rep2
GSM759860 E10.5_forelimb_ChIP_input_rep3
BioProject PRJNA144639
SRA SRP007492

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Supplementary file Size Download File type/resource
GSE30641_RAW.tar 36.6 Gb (http)(custom) TAR (of BED, BW, SAM)
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Raw data are available in SRA
Processed data provided as supplementary file

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