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Series GSE23436 Query DataSets for GSE23436
Status Public on Nov 17, 2010
Title Histone methylation and transcription factor binding during intestinal cell differentation
Organisms Homo sapiens; Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by array
Summary Cell differentiation requires epigenetic modulation of tissue-specific genes and activities of master transcriptional regulators, which are recognized for their dominant control over cellular programs. Using novel epigenomic methods, we characterized enhancer elements specifically modified in differentiating intestinal epithelial cells and found enrichment of transcription factor-binding motifs corresponding to CDX2, a master regulator of the intestine. Directed investigation revealed surprising lability in CDX2 occupancy of the genome, with redistribution from hundreds of sites occupied only in progenitors to thousands of new sites in mature cells. Knockout mice confirmed distinct Cdx2 requirements in dividing and differentiated adult intestinal cells, including responsibility for the active enhancer configuration associated with maturity. Dynamic CDX2 occupancy corresponds with condition-specific gene expression and, importantly, to differential co-occupancy with other tissue-restricted transcription factors: HNF4A in mature cells and GATA6 in progenitors. These results reveal dynamic, context-specific functions and mechanisms of a master transcription factor within a cell lineage.
Overall design H3K4me2, CDX2, GATA6, and HNF4A ChIP-seq patterns were mapped in proliferating and 26 day post-confluent (differentatied) Caco-2 intestinal cell lines and compared to published expression data or newly generated Cdx2 knockout mouse intestine expression data
Contributor(s) Shivdasani RA, Liu XS, Shin H, Verzi MP
Citation(s) 21074721
Submission date Aug 05, 2010
Last update date May 15, 2019
Contact name Michael P Verzi
Organization name Rutgers, the State University of New Jersey
Department Genetics
Lab Verzi
Street address 145 Bevier Road
City Piscataway
State/province NJ
ZIP/Postal code 08854
Country USA
Platforms (2)
GPL9115 Illumina Genome Analyzer II (Homo sapiens)
GPL10773 [Mouse430_2_Mm_REFSEQ] Affymetrix GeneChip Mouse Genome 430 2.0 Array [Brainarray Version 12]
Samples (17)
GSM575222 H3K4me2 in proliferating cells
GSM575223 H3K4me2 in differentated cells
GSM575224 CDX2 ChIP-seq in proliferating cells
SRA SRP003411
BioProject PRJNA131107

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Supplementary file Size Download File type/resource
GSE23436_RAW.tar 964.6 Mb (http)(custom) TAR (of BED, BW, CEL, TXT)
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Processed data provided as supplementary file
Processed data included within Sample table
Raw data are available in SRA

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