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Promoter capture Hi-C-based identification of recurrent noncoding mutations in colorectal cancer
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Promoter capture Hi-C-based identification of recurrent noncoding mutations in colorectal cancer
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Promoter capture Hi-C-based identification of recurrent noncoding mutations in colorectal cancer
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Journal Article
Promoter capture Hi-C-based identification of recurrent noncoding mutations in colorectal cancer
2018
Overview
Efforts are being directed to systematically analyze the non-coding regions of the genome for cancer-driving mutations
1
–
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 Atlas
7
,
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 amplification
1
. 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.
Promoter capture Hi-C in colorectal cancer cells integrated with cancer genome and expression data identifies a noncoding, cis-regulatory element that is recurrently mutated in cancer, affecting
ETV1
expression, cell viability and patient survival.
Publisher
Nature Publishing Group US,Nature Publishing Group
Subject
/ 13/106
/ 13/109
/ 13/31
/ 13/44
/ 13/89
/ 38
/ 38/22
/ 38/39
/ 38/77
/ 38/90
/ 38/91
/ 45
/ Animal Genetics and Genomics
/ Biomedical and Life Sciences
/ Cancer
/ Cell Transformation, Neoplastic - genetics
/ Chromosomes, Human - chemistry
/ Colorectal Neoplasms - epidemiology
/ Colorectal Neoplasms - genetics
/ Computational Biology - methods
/ DNA
/ Genes
/ Genomes
/ Genomics
/ High-Throughput Nucleotide Sequencing - methods
/ Humans
/ Letter
/ Mutation
/ Promoter Regions, Genetic - genetics
/ Regulatory Sequences, Nucleic Acid - genetics
/ Tumors
