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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

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)

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)

More...

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)

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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

GSM560219	CDX2 ChIP-chip in CaCo2 Array B Rep 1
GSM560220	CDX2 ChIP-chip in CaCo2 Array B Rep 2
GSM560221	CDX2 ChIP-chip in CaCo2 Array B Rep 3
GSM560222	CDX2 ChIP-chip in CaCo2 Array C Rep 1
GSM560223	CDX2 ChIP-chip in CaCo2 Array C Rep 2
GSM560224	CDX2 ChIP-chip in CaCo2 Array C Rep 3
GSM560225	CDX2 ChIP-chip in CaCo2 Array D Rep 1
GSM560226	CDX2 ChIP-chip in CaCo2 Array D Rep 2
GSM560227	CDX2 ChIP-chip in CaCo2 Array D Rep 3
GSM560228	CDX2 ChIP-chip in CaCo2 Array E Rep 1
GSM560229	CDX2 ChIP-chip in CaCo2 Array E Rep 2
GSM560230	CDX2 ChIP-chip in CaCo2 Array E Rep 3
GSM560231	CDX2 ChIP-chip in CaCo2 Array F Rep 1
GSM560232	CDX2 ChIP-chip in CaCo2 Array F Rep 2
GSM560233	CDX2 ChIP-chip in CaCo2 Array F Rep 3
GSM560234	CDX2 ChIP-chip in CaCo2 Array G Rep 1
GSM560235	CDX2 ChIP-chip in CaCo2 Array G Rep 2
GSM560236	CDX2 ChIP-chip in CaCo2 Array G Rep 3
GSM560237	TCF4 ChIP-chip in CaCo2 Array F Rep 1
GSM560238	TCF4 ChIP-chip in CaCo2 Array F Rep 2
GSM560239	TCF4 ChIP-chip in Ls174t Array F Rep 1
GSM560240	TCF4 ChIP-chip in Ls174t Array F Rep 2
GSM560241	CDX2 ChIP-chip in Ls174t Array F Rep 1
GSM560242	CDX2 ChIP-chip in Ls174t Array F Rep 2
GSM560243	IgG control CHIP in CaCo2 array A Rep 1
GSM560244	IgG control CHIP in CaCo2 array A Rep 2
GSM560245	IgG control CHIP in CaCo2 array A Rep 3
GSM560246	IgG control CHIP in CaCo2 array B Rep 1
GSM560247	IgG control CHIP in CaCo2 array B Rep 2
GSM560248	IgG control CHIP in CaCo2 array B Rep 3
GSM560249	IgG control CHIP in CaCo2 array C Rep 1
GSM560250	IgG control CHIP in CaCo2 array C Rep 2
GSM560251	IgG control CHIP in CaCo2 array C Rep 3
GSM560252	IgG control CHIP in CaCo2 array D Rep 1
GSM560253	IgG control CHIP in CaCo2 array D Rep 2
GSM560254	IgG control CHIP in CaCo2 array D Rep 3
GSM560255	IgG control CHIP in CaCo2 array E Rep 1
GSM560256	IgG control CHIP in CaCo2 array E Rep 2
GSM560257	IgG control CHIP in CaCo2 array E Rep 3
GSM560258	IgG control CHIP in CaCo2 array F Rep 1
GSM560259	IgG control CHIP in CaCo2 array F Rep 2
GSM560260	IgG control CHIP in CaCo2 array F Rep 3
GSM560261	IgG control CHIP in CaCo2 array G Rep 1
GSM560262	IgG control CHIP in CaCo2 array G Rep 2
GSM560263	IgG control CHIP in CaCo2 array G Rep 3
GSM560264	Input Ls174t array F Rep 1
GSM560265	Input Ls174t array F Rep 2
GSM560266	Input Ls174t array F Rep 3
GSM564444	shGFP1
GSM564445	shCDX2-2
GSM564446	shCDX2-4
GSM564447	shGFP2
GSM564448	shCDX2-2b

Relations

BioProject

Download family	Format
SOFT formatted family file(s)	SOFT
MINiML formatted family file(s)	MINiML
Series Matrix File(s)	TXT

Supplementary file	Size	Download	File type/resource
GSE22572_RAW.tar	1.2 Gb	(http)(custom)	TAR (of CEL)
GSE22572_TCF4ls174tn2input3.Hs35b_P06R_v01-3_NCBIv36.NR.bpmap_matscore.bar.gz	33.4 Mb	(ftp)(http)	BAR
GSE22572_TCF4ls174tn2input3.Hs35b_P06R_v01-3_NCBIv36.NR.bpmap_matscore.bar.txt.gz	38.5 Mb	(ftp)(http)	TXT
GSE22572_cdxLs174tFnof2.Hs35b_P06R_v01-3_NCBIv36.NR.bpmap_matscore.bar.gz	33.4 Mb	(ftp)(http)	BAR
GSE22572_cdxLs174tFnof2.Hs35b_P06R_v01-3_NCBIv36.NR.bpmap_matscore.bar.txt.gz	38.5 Mb	(ftp)(http)	TXT
GSE22572_shCDX2knockdownDataProcessedWith_dChip.txt.gz	36.7 Kb	(ftp)(http)	TXT
GSE22572_tcf4cacoFduplicate.Hs35b_P06R_v01-3_NCBIv36.NR.bpmap_matscore.bar.gz	33.4 Mb	(ftp)(http)	BAR
GSE22572_tcf4cacoFduplicate.Hs35b_P06R_v01-3_NCBIv36.NR.bpmap_matscore.bar.txt.gz	38.3 Mb	(ftp)(http)	TXT
GSE22572_triplicate.Hs35b_P01R_v01-3_NCBIv36.NR.bpmap_matscore.bar.gz	33.0 Mb	(ftp)(http)	BAR
GSE22572_triplicate.Hs35b_P01R_v01-3_NCBIv36.NR.bpmap_matscore.bar.txt.gz	37.9 Mb	(ftp)(http)	TXT
GSE22572_triplicate.Hs35b_P02R_v01-3_NCBIv36.NR.bpmap_matscore.bar.gz	34.0 Mb	(ftp)(http)	BAR
GSE22572_triplicate.Hs35b_P02R_v01-3_NCBIv36.NR.bpmap_matscore.bar.txt.gz	39.1 Mb	(ftp)(http)	TXT
GSE22572_triplicate.Hs35b_P03R_v01-3_NCBIv36.NR.bpmap_matscore.bar.gz	33.2 Mb	(ftp)(http)	BAR
GSE22572_triplicate.Hs35b_P03R_v01-3_NCBIv36.NR.bpmap_matscore.bar.txt.gz	38.3 Mb	(ftp)(http)	TXT
GSE22572_triplicate.Hs35b_P04R_v01-3_NCBIv36.NR.bpmap_matscore.bar.gz	33.9 Mb	(ftp)(http)	BAR
GSE22572_triplicate.Hs35b_P04R_v01-3_NCBIv36.NR.bpmap_matscore.bar.txt.gz	39.1 Mb	(ftp)(http)	TXT
GSE22572_triplicate.Hs35b_P05R_v01-3_NCBIv36.NR.bpmap_matscore.bar.gz	33.9 Mb	(ftp)(http)	BAR
GSE22572_triplicate.Hs35b_P05R_v01-3_NCBIv36.NR.bpmap_matscore.bar.txt.gz	39.0 Mb	(ftp)(http)	TXT
GSE22572_triplicate.Hs35b_P06R_v01-3_NCBIv36.NR.bpmap_matscore.bar.gz	33.4 Mb	(ftp)(http)	BAR
GSE22572_triplicate.Hs35b_P06R_v01-3_NCBIv36.NR.bpmap_matscore.bar.txt.gz	38.4 Mb	(ftp)(http)	TXT
GSE22572_triplicate.Hs35b_P07R_v01-3_NCBIv36.NR.bpmap_matscore.bar.gz	33.2 Mb	(ftp)(http)	BAR
GSE22572_triplicate.Hs35b_P07R_v01-3_NCBIv36.NR.bpmap_matscore.bar.txt.gz	38.4 Mb	(ftp)(http)	TXT
Processed data are available on Series record
Processed data included within Sample table

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