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Elife. 2017 Oct 2;6. pii: e30506. doi: 10.7554/eLife.30506.

Chromatin accessibility underlies synthetic lethality of SWI/SNF subunits in ARID1A-mutant cancers.

Author information

1
Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, California, United States.
2
The Razavi Newman Integrative Genomics and Bioinformatics Core Facility, Salk Institute for Biological Studies, California, United States.
3
Department of Medicine, University of California San Diego, California, United States.

Abstract

ARID1A, a subunit of the SWI/SNF chromatin remodeling complex, is frequently mutated in cancer. Deficiency in its homolog ARID1B is synthetically lethal with ARID1A mutation. However, the functional relationship between these homologs has not been explored. Here, we use ATAC-seq, genome-wide histone modification mapping, and expression analysis to examine colorectal cancer cells lacking one or both ARID proteins. We find that ARID1A has a dominant role in maintaining chromatin accessibility at enhancers, while the contribution of ARID1B is evident only in the context of ARID1A mutation. Changes in accessibility are predictive of changes in expression and correlate with loss of H3K4me and H3K27ac marks, nucleosome spacing, and transcription factor binding, particularly at growth pathway genes including MET. We find that ARID1B knockdown in ARID1A mutant ovarian cancer cells causes similar loss of enhancer architecture, suggesting that this is a conserved function underlying the synthetic lethality between ARID1A and ARID1B.

KEYWORDS:

ARID1A; ARID1B; SWI/SNF complex; chromatin accessibility; chromatin remodeling; chromosomes; epigenetics; genes; human

PMID:
28967863
PMCID:
PMC5643100
DOI:
10.7554/eLife.30506
[Indexed for MEDLINE]
Free PMC Article

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