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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 16, 2014 |
| Title |
Obesity, rather than diet, drives epigenomic alterations in colonic epithelium resembling cancer progression |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
High-fat diet and obesity are high risk factors for colorectal cancer. The underlying mechanism is still unclear. Environmental factors alter the epigenome to affect gene expression thus the phenotype. In response to external stimuli, the cis-regulatory regions, especially enhancer loci, are key elements for regulating selective gene expression. We thus explored the effects of high-fat diet and the accompanying obesity on gene expression and the enhancer landscape in colon epithelium. High-fat diet exposed binding sites of transcription factors downstream of signaling pathways important in the initiation and progression of colon cancer. Meantime, colon specific enhancers were lost rendering the cells potential for dedifferentiation. The alteration at enhancer regions drives a specific transcription program promoting colon cancer progression. The comprehensive interrogation of enhancer changes by high-fat diet in colon epithelium provides a number of insights into the underlying biology of high-fat diet and obesity in increasing colon cancer risk, and provides potential therapeutic targets to treat obese colon cancer patients.
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| Overall design |
ChIP sequencing of active enhancer mark h3k27ac in colon epithelium from wild type mice and NAG-1 transgenic mice treated with either low-fat diet or high-fat diet.
The gene expression component of the study is included in GSE46843.
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| Contributor(s) |
Li R, Wade PA, Grimm S |
| Citation(s) |
24703701 |
| Submission date |
May 08, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
ruifang li |
| E-mail(s) |
lir4@niehs.nih.gov
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| Organization name |
NIEHS
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| Street address |
111 T.W. Alexander Drive
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| City |
RTP |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
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| Platforms (2) |
| GPL11002 |
Illumina Genome Analyzer IIx (Mus musculus) |
| GPL16417 |
Illumina MiSeq (Mus musculus) |
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| Samples (18)
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| Relations |
| BioProject |
PRJNA202232 |
| SRA |
SRP022181 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE46748_RAW.tar |
1.7 Gb |
(http)(custom) |
TAR (of BED, BEDGRAPH) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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