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Epigenomic enhancer profiling defines a signature of colon cancer

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE36401 | GEO | 2012/04/16

SECONDARY ACCESSION(S): PRJNA153293

REPOSITORIES: GEO

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Epigenomic enhancer profiling defines a signature of colon cancer.

Project description:Cancer is characterized by gene expression aberrations. Studies have largely focused on coding sequences and promoters, even though distal regulatory elements play a central role in controlling transcription patterns. We used 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 specific transcriptional program to promote colon carcinogenesis.

| S-EPMC3711120 | biostudies-literature

Epigenomic enhancer profiling defines a signature of colon cancer

Project description:This SuperSeries is composed of the following subset Series: GSE36204: Epigenomic enhancer profiling defines a signature of colon cancer [ChIP-seq] GSE36400: All exon array expression data in normal colon and primary colon cancer lines [expression] Refer to individual Series

2012-04-15 | E-GEOD-36401 | biostudies-arrayexpress

Epigenomic enhancer profiling defines a signature of colon cancer [ChIP-seq]

Project description: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. Examination of 3 histone modifications and global expression data in primary colon cancer cell lines and normal colon crypt controls

2012-04-15 | E-GEOD-36204 | biostudies-arrayexpress

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