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Series GSE25426 Query DataSets for GSE25426
Status Public on Dec 01, 2011
Title Functional and cellular constraints that shaped the PPARg binding landscape in human and mouse macrophages: human ChIP-Seq
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Genome-wide comparisons of transcription factor binding sites in different species allow for a direct evaluation of the evolutionary constraints that shape transcription factor binding landscapes. To gain insights into the evolution of the PPARg-dependent transcriptional network, we obtained binding data for PPARg, RXR and PU.1 in human macrophages and compared the profiles to matching data from mouse macrophages (Lefterova et al. 2010 (PMID 20176806); GSE21314). We found that PPARg binding was highly divergent and only 5% of the PPARg-bound regions were occupied in both species. Despite the low conservation of PPARg binding sites, conserved PPARg target genes contribute more than 30% to the functional target genes identified in human macrophages. In addition, conserved target genes are strongly enriched for lipid metabolic functions. We detected the lineage-specification factor PU.1 at the majority of human PPARg binding sites. This confirmed the juxtaposed binding configuration found in mouse macrophages and demonstrated the preservation of tissue-specific adjacent PPARg-Pu.1 binding in the absence of individual binding site conservation. Finally, based on this PPARg and PU.1 binding between human and mouse, we suggest a mechanism by which PU.1 facilitates PPARg binding site turnover in macrophages.
Overall design Genome-wide location analysis for 3 transcription factors (PPARg, RXR and PU.1) in a human monocytic cell line (THP-1).

This submission represents the human binding data component of the study.
Contributor(s) Pott S, Liu ET
Citation(s) 23118933
Submission date Nov 16, 2010
Last update date May 15, 2019
Contact name Sebastian Pott
Organization name University of Chicago
Department Human Genetics
Street address 920 58th Street
City Chicago
State/province Il
ZIP/Postal code 60637
Country USA
Platforms (1)
GPL9052 Illumina Genome Analyzer (Homo sapiens)
Samples (4)
GSM624141 PPARg_ChIPseq
GSM624142 RXR_ChIPseq
GSM624143 PU.1_ChIPseq
This SubSeries is part of SuperSeries:
GSE25608 Functional and cellular constraints that shaped the PPARg binding landscape in human and mouse macrophages
SRA SRP009091
BioProject PRJNA142611

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
GSE25426_RAW.tar 2.0 Gb (http)(custom) TAR (of TXT)
GSE25426_readme.txt 1.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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