The chromatin accessibility landscape of primary human cancers
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Abstract
We present the genome-wide chromatin accessibility profiles of 410 tumor samples spanning 23 cancer types from The Cancer Genome Atlas (TCGA). We identify 562,709 transposase-accessible DNA elements that substantially extend the compendium of known cis-regulatory elements. Integration of ATAC-seq (the assay for transposase-accessible chromatin using sequencing) with TCGA multi-omic data identifies a large number of putative distal enhancers that distinguish molecular subtypes of cancers, uncovers specific driving transcription factors via protein-DNA footprints, and nominates long-range gene-regulatory interactions in cancer. These data reveal genetic risk loci of cancer predisposition as active DNA regulatory elements in cancer, identify gene-regulatory interactions underlying cancer immune evasion, and pinpoint noncoding mutations that drive enhancer activation and may affect patient survival. These results suggest a systematic approach to understanding the noncoding genome in cancer to advance diagnosis and therapy.
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The record
- Venue
- Science
- Topic
- Cancer Genomics and Diagnostics
- Field
- Biochemistry, Genetics and Molecular Biology
- Canadian institutions
- Canada's Michael Smith Genome Sciences CentreBC Cancer Agency
- Funders
- National Cancer InstituteNational Institute on AgingNational Institutes of HealthNational Human Genome Research InstituteHoward Hughes Medical Institute
- Keywords
- ChromatinPrimary (astronomy)Computational biologyBiologyGeographyGeneticsDNAPhysics
- Has abstract in OpenAlex
- yes