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Series GSE22572 Query DataSets for GSE22572
Status Public on Aug 11, 2010
Title TCF4 and CDX2, major transcription factors for intestinal function, converge on the same cis-regulatory regions
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by genome tiling array
Expression profiling by array
Summary Surprisingly few pathways signal between cells, raising questions about mechanisms for tissue-specific responses. In particular, Wnt ligands signal in many mammalian tissues, including the intestinal epithelium, where constitutive signaling causes cancer. Genome-wide analysis of DNA cis-regulatory regions bound by the intestine-restricted transcription factor CDX2 in colonic cells uncovered highly significant over-representation of sequences that bind TCF4, a transcriptional effector of intestinal Wnt signaling. Chromatin immunoprecipitation confirmed TCF4 occupancy at most such sites and co-occupancy of CDX2 and TCF4 across short distances. A region spanning the single nucleotide polymorphism rs6983267, which lies within a MYC enhancer and confers colorectal cancer risk in humans, represented one of many co-occupied sites. Co-occupancy correlated with intestine-specific gene expression and CDX2 loss reduced TCF4 binding.These results implicate CDX2 in directing TCF4 binding in intestinal cells. Co-occupancy of regulatory regions by signal-effector and tissue-restricted transcription factors may represent a general mechanism for ubiquitous signaling pathways to achieve tissue-specific outcomes.
Overall design A series of ChIP-chip experiments identified the CDX2 cistrome and discovered and validated extensive co-binding with TCF4 in colon cancer cell lines

Transcriptional profiling following shRNA-mediated CDX2 knockdown was employed to identify CDX2-dependent gene expression in the human colon cancer cell line Caco2
Contributor(s) Michael V, Ramesh S
Citation(s) 20696899
Submission date Jun 25, 2010
Last update date Mar 25, 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 (8)
GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
GPL4910 [Hs35b_P01R] Affymetrix Human Tiling 2.0R Set, Array 1
GPL4911 [Hs35b_P02R] Affymetrix Human Tiling 2.0R Set, Array 2
Samples (56)
GSM560216 CDX2 ChIP-chip in CaCo2 Array A Rep 1
GSM560217 CDX2 ChIP-chip in CaCo2 Array A Rep 2
GSM560218 CDX2 ChIP-chip in CaCo2 Array A Rep 3
BioProject PRJNA128423

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
GSE22572_RAW.tar 1.2 Gb (http)(custom) TAR (of CEL) 33.4 Mb (ftp)(http) BAR 38.5 Mb (ftp)(http) TXT 33.4 Mb (ftp)(http) BAR 38.5 Mb (ftp)(http) TXT
GSE22572_shCDX2knockdownDataProcessedWith_dChip.txt.gz 36.7 Kb (ftp)(http) TXT 33.4 Mb (ftp)(http) BAR 38.3 Mb (ftp)(http) TXT 33.0 Mb (ftp)(http) BAR 37.9 Mb (ftp)(http) TXT 34.0 Mb (ftp)(http) BAR 39.1 Mb (ftp)(http) TXT 33.2 Mb (ftp)(http) BAR 38.3 Mb (ftp)(http) TXT 33.9 Mb (ftp)(http) BAR 39.1 Mb (ftp)(http) TXT 33.9 Mb (ftp)(http) BAR 39.0 Mb (ftp)(http) TXT 33.4 Mb (ftp)(http) BAR 38.4 Mb (ftp)(http) TXT 33.2 Mb (ftp)(http) BAR 38.4 Mb (ftp)(http) TXT
Processed data are available on Series record
Processed data included within Sample table

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