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Series GSE51336 Query DataSets for GSE51336
Status Public on Nov 20, 2014
Title Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution
Organisms Homo sapiens; Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary To study the evolutionary dynamics of regulatory DNA, we mapped >1.3 million deoxyribonuclease I–hypersensitive sites (DHSs) in 45 mouse cell and tissue types, and systematically compared these with human DHS maps from orthologous compartments. We found that the mouse and human genomes have undergone extensive cis-regulatory rewiring that combines branch-specific evolutionary innovation and loss with widespread repurposing of conserved DHSs to alternative cell fates, and that this process is mediated by turnover of transcription factor (TF) recognition elements. Despite pervasive evolutionary remodeling of the location and content of individual cis-regulatory regions, within orthologous mouse and human cell types the global fraction of regulatory DNA bases encoding recognition sites for each TF has been strictly conserved. Our findings provide new insights into the evolutionary forces shaping mammalian regulatory DNA landscapes.
 
Overall design To study the evolutionary dynamics of regulatory DNA, we mapped >1.3 million deoxyribonuclease I–hypersensitive sites (DHSs) in 45 mouse cell and tissue types, and systematically compared these with human DHS maps from orthologous compartments.
 
Contributor(s) Vierstra J, Rynes E, Sandstrom R, Thurman RE, Zhang M, Canfield T, Sabo PJ, Byron R, Hansen RS, Johnson AK, Vong S, Lee K, Bates D, Neri F, Diegel M, Giste E, Haugen E, Dunn D, Humbert R, Wilken MS, Josefowicz S, Samstein R, Chang K, Levassuer D, Disteche C, De Bruijn M, Rey TA, Skoultchi A, Rudensky A, Orkin SH, Papayannopoulou T, Treuting P, Selleri L, Kaul R, Bender MA, Groudine M, Stamatoyannopoulos JA
Citation(s) 25411453
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 (5)
GPL9052 Illumina Genome Analyzer (Homo sapiens)
GPL9115 Illumina Genome Analyzer II (Homo sapiens)
GPL9185 Illumina Genome Analyzer (Mus musculus)
Samples (266)
GSM530651 Chromatin accessibility assay of Fetal Brain Primary Tissue; DS11872
GSM530653 Chromatin accessibility assay of Fetal Adrenal Primary Tissue; DS12528
GSM530654 Chromatin accessibility assay of Fetal Heart Primary Tissue; DS12531
Relations
BioProject PRJNA267839

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
GSE51336_RAW.tar 230.4 Gb (http)(custom) TAR (of BAM, BED, BIGWIG, BROADPEAK, NARROWPEAK, WIG)
SRA Run SelectorHelp
Raw data provided as supplementary file
Processed data provided as supplementary file
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