4.8 Article

DNase I-hypersensitive exons colocalize with promoters and distal regulatory elements

Journal

NATURE GENETICS
Volume 45, Issue 8, Pages 852-U181

Publisher

NATURE PUBLISHING GROUP
DOI: 10.1038/ng.2677

Keywords

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Funding

  1. Australian National Health and Medical Research Council [631668, 631381, 1021731]
  2. Queensland State Government (National and International Research Alliance Program)
  3. National Breast Cancer Foundation Australia
  4. National Human Genome Research Institute (NHGRI) [HG004456]
  5. US National Institutes of Health (NHGRI) [U54HG004592, U54HG007599]

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The precise splicing of genes confers an enormous transcriptional complexity to the human genome. The majority of gene splicing occurs cotranscriptionally, permitting epigenetic modifications to affect splicing outcomes. Here we show that select exonic regions are demarcated within the three-dimensional structure of the human genome. We identify a subset of exons that exhibit DNase I hypersensitivity and are accompanied by 'phantom' signals in chromatin immunoprecipitation and sequencing (ChIP-seq) that result from cross-linking with proximal promoter- or enhancer-bound factors. The capture of structural features by ChIP-seq is confirmed by chromatin interaction analysis that resolves local intragenic loops that fold exons close to cognate promoters while excluding intervening intronic sequences. These interactions of exons with promoters and enhancers are enriched for alternative splicing events, an effect reflected in cell type-specific periexonic DNase I hypersensitivity patterns. Collectively, our results connect local genome topography, chromatin structure and cis-regulatory landscapes with the generation of human transcriptional complexity by cotranscriptional splicing.

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