|
| Status |
Public on Apr 16, 2012 |
| Title |
Epigenomic enhancer profiling defines a signature of colon cancer [ChIP-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Cancer is characterized by gene expression aberrations. Studies have largely focused on coding sequences and promoters, despite the fact that distal regulatory elements play a central role in controlling transcription patterns. Here we utilize the histone mark H3K4me1 to analyze gain and loss of enhancer activity genome wide in primary colon cancer lines relative to normal colon crypts. We identified thousands of variant enhancer loci (VELs) that comprise a signature that is robustly predictive of the in vivo colon cancer transcriptome. Furthermore, VELs are enriched in haplotype blocks containing colon cancer genetic risk variants, implicating these genomic regions in colon cancer pathogenesis. We propose that reproducible changes in the epigenome at enhancer elements drive a unique transcriptional program to promote colon carcinogenesis.
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| |
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| Overall design |
Examination of 3 histone modifications and global expression data in primary colon cancer cell lines and normal colon crypt controls
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| |
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| Contributor(s) |
Akhtar-Zaidi B, Saiakhova A, Scacheri PC |
| Citation(s) |
22499810 |
| Submission date |
Mar 01, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Peter Scacheri |
| E-mail(s) |
pxs183@case.edu
|
| Phone |
216-368-3458
|
| Organization name |
Case Western Reserve University
|
| Street address |
10900 Euclid Ave; BRB 647
|
| City |
Cleveland Heights |
| State/province |
OH |
| ZIP/Postal code |
44106 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL10999 |
Illumina Genome Analyzer IIx (Homo sapiens) |
|
| Samples (41)
|
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| This SubSeries is part of SuperSeries: |
| GSE36401 |
Epigenomic enhancer profiling defines a signature of colon cancer |
|
| Relations |
| SRA |
SRP011188 |
| BioProject |
PRJNA155759 |
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