Promoter capture Hi-C-based identification of recurrent noncoding mutations in colorectal cancer.
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Authors
Orlando, G
Law, PJ
Cornish, AJ
Dobbins, SE
Chubb, D
Broderick, P
Litchfield, K
Hariri, F
Pastinen, T
Osborne, CS
Taipale, J
Houlston, RS
Law, PJ
Cornish, AJ
Dobbins, SE
Chubb, D
Broderick, P
Litchfield, K
Hariri, F
Pastinen, T
Osborne, CS
Taipale, J
Houlston, RS
Document Type
Journal Article
Date
2018-10-01
Date Accepted
2018-07-27
Abstract
Efforts are being directed to systematically analyze the non-coding regions of the genome for cancer-driving mutations1-6. cis-regulatory elements (CREs) represent a highly enriched subset of the non-coding regions of the genome in which to search for such mutations. Here we use high-throughput chromosome conformation capture techniques (Hi-C) for 19,023 promoter fragments to catalog the regulatory landscape of colorectal cancer in cell lines, mapping CREs and integrating these with whole-genome sequence and expression data from The Cancer Genome Atlas7,8. We identify a recurrently mutated CRE interacting with the ETV1 promoter affecting gene expression. ETV1 expression influences cell viability and is associated with patient survival. We further refine our understanding of the regulatory effects of copy-number variations, showing that RASL11A is targeted by a previously identified enhancer amplification1. This study reveals new insights into the complex genetic alterations driving tumor development, providing a paradigm for employing chromosome conformation capture to decipher non-coding CREs relevant to cancer biology.
Citation
Nature genetics, 2018, 50 (10), pp. 1375 - 1380
Source Title
Publisher
NATURE PORTFOLIO
ISSN
1061-4036
eISSN
1546-1718
Collections
Research Team
Cancer Genomics
Molecular & Population Genetics
Molecular & Population Genetics