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| Status |
Public on May 10, 2007 |
| Title |
Mapping of HNF4α binding sites, acetylation of histone H3 and expression in Caco2 cells |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
Genome binding/occupancy profiling by genome tiling array
|
| Summary |
Background & Aims: The role of HNF4α has been extensively studied in hepatocytes and pancreatic β cells, but emerging evidence indicates that HNF4α is a key regulator of intestinal epithelial cell differentiation as well. The aim of the present work is to identify HNF4α target genes in the intestine in order to elucidate the role of HNF4α in differentiation of the intestinal epithelial cells. Results: One thousand one hundred and seventy-six genes were identified as HNF4α targets, many of which have not previously been described as being regulated by HNF4α. The 1,176 genes contributed significantly to gene ontology (GO) pathways categorized by lipid and amino acid transport and metabolism. A thorough analysis of Cdx-2, trehalase, and cingulin promoters verified that these genes are regulated by HNF4α. In each case we were able to identify a functional HNF4α binding site in their promoters. Conclusions: HNF4α regulation of the Cdx-2 promoter unravels a transcription factor network also including HNF1α and β, all of which are transcription factors involved in intestinal development and gene expression.
Keywords: ChIP-CHIP and expression data
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| Overall design |
Methods: We have performed a ChIP-chip analysis of the human intestinal cell line Caco-2 in order to make a genome-wide identification of HNF4α binding to promoter regions. The HNF4α ChIP-chip data was matched with gene expression and histone H3 acetylation status of the promoters in order to identify HNF4α binding to actively transcribed genes with an open chromatin structure.
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| Contributor(s) |
Nielsen M, Bressendorff S, Møller J, Olsen J, Troelsen JT |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
May 07, 2007 |
| Last update date |
Mar 25, 2019 |
| Contact name |
Jesper T Troelsen |
| E-mail(s) |
troelsen@imbg.ku.dk
|
| Organization name |
Univ. of Copenhagen
|
| Street address |
Blegdamsvej 3b
|
| City |
Copenhagen |
| ZIP/Postal code |
Dk-2200 |
| Country |
Denmark |
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| Platforms (2) |
| GPL570 |
[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array |
| GPL5139 |
Nimblegen Homo sapiens promoter array hg17 |
|
| Samples (12)
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| GSM187238 |
HNF4a chip chip on Caco-2 cells replica 1 |
| GSM187444 |
HNF4a chip chip on Caco-2 cells replica 2 |
| GSM187445 |
HNF4a chip chip on Caco-2 cells replica 3 |
| GSM187449 |
Achis 3 ChIp chip analysis on Caco-2 cells replica 2 |
| GSM187455 |
Achis 3 ChIp chip analysis on Caco-2 cells replica 1 |
| GSM187457 |
Achis 3 ChIp chip analysis on Caco-2 cells replica 3 |
| GSM187459 |
Expression analysis of undifferentiated Caco-2 replica 1 |
| GSM187460 |
Expression analysis of undifferentiated Caco-2 replica 2 |
| GSM187461 |
Expression analysis of undifferentiated Caco-2 replica 3 |
| GSM187694 |
Expression analysis of differentiated Caco-2 replica 1 |
| GSM187695 |
Expression analysis of differentiated Caco-2 replica 2 |
| GSM187696 |
Expression analysis of differentiated Caco-2 replica 3 |
|
| Relations |
| BioProject |
PRJNA99859 |
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