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Series GSE51341 Query DataSets for GSE51341
Status Public on Nov 19, 2014
Title Conservation of mouse-human trans-regulatory circuitry despite high cis-regulatory divergence
Organisms Homo sapiens; Mus musculus
Experiment type Other
Summary The basic body plan and major physiological axes have been highly conserved during mammalian evolution, yet only a small fraction of the human genome sequence appears to be subject to evolutionary constraint. To quantify cis- versus trans-acting contributions to mammalian regulatory evolution, we performed genomic DNase I footprinting of the mouse genome across 25 cell and tissue types, collectively defining ~8.6 million transcription factor (TF) occupancy sites at nucleotide resolution. Here we show that mouse TF footprints conjointly encode a regulatory lexicon that is ~95% similar with that derived from human TF footprints. However, only ~20% of mouse TF footprints have human orthologues. Despite substantial turnover of the cis-regulatory landscape, nearly half of all pairwise regulatory interactions connecting mouse TF genes have been maintained in orthologous human cell types through
evolutionary innovation of TF recognition sequences. Furthermore, the higher-level organization of mouse TF-to-TF connections into cellular network architectures is nearly identical with human. Our results indicate that evolutionary selection on mammalian gene regulation is targeted chiefly at the level of trans-regulatory circuitry, enabling and potentiating cis-regulatory plasticity.
 
Overall design We performed genomic DNase I footprinting of the mouse genome across 25 cell and tissue types, collectively defining ~8.6 million transcription factor (TF) occupancy sites at nucleotide resolution.
 
Contributor(s) Stamatoyannopoulos JA
Citation(s) 25409825
Submission date Oct 02, 2013
Last update date May 15, 2019
Contact name ENCODE DCC
E-mail(s) encode-help@lists.stanford.edu
Organization name ENCODE DCC
Street address 300 Pasteur Dr
City Stanford
State/province CA
ZIP/Postal code 94305-5120
Country USA
 
Platforms (6)
GPL9115 Illumina Genome Analyzer II (Homo sapiens)
GPL9185 Illumina Genome Analyzer (Mus musculus)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
Samples (32)
GSM646563 UW_DnaseDgf_H7-hESC
GSM646567 Stam_K562
GSM723021 Digital Genomic Footprinting assay of Fetal Brain; DGF.DS11872
Relations
BioProject PRJNA267242

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
GSE51341_RAW.tar 53.6 Gb (http)(custom) TAR (of BAM, BED, BIGWIG, BROADPEAK, NARROWPEAK, TXT, WIG)
SRA Run SelectorHelp
Raw data provided as supplementary file
Processed data provided as supplementary file

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