Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

All exon array expression data in normal colon and primary colon cancer lines [expression]

ABSTRACT: 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. We used gene expression profiles to assess correlations between the colon cancer epigenome and transcriptional activity. RNA from normal colon epithelial crypt controls and primary colon cancer cell lines was hybridized to Affymetrix All Exon Human ST 1.0 microarrays.

ORGANISM(S): Homo sapiens

SUBMITTER: Peter Scacheri

PROVIDER: E-GEOD-36400 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Epigenomic enhancer profiling defines a signature of colon cancer.

Akhtar-Zaidi Batool B Cowper-Sal-lari Richard R Corradin Olivia O Saiakhova Alina A Bartels Cynthia F CF Balasubramanian Dheepa D Myeroff Lois L Lutterbaugh James J Jarrar Awad A Kalady Matthew F MF Willis Joseph J Moore Jason H JH Tesar Paul J PJ Laframboise Thomas T Markowitz Sanford S Lupien Mathieu M Scacheri Peter C PC

Science (New York, N.Y.) 20120412 6082

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 col ...[more]

PMID: 22499810

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Dataset Information

All exon array expression data in normal colon and primary colon cancer lines [expression]

Publications

Epigenomic enhancer profiling defines a signature of colon cancer.

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