DNase I-hypersensitive exons colocalize with promoters and distal regulatory elements.
Document Type
Article
Publication Date
8-2013
JAX Source
Nat Genet 2013 Aug; 45(8):852-9.
Volume
45
Issue
8
First Page
852
Last Page
859
ISSN
1546-1718
PMID
23793028
Abstract
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. Nat Genet 2013 Aug; 45(8):852-9.
Recommended Citation
Mercer T,
Edwards S,
Clark M,
Neph S,
Wang H,
Stergachis A,
John S,
Sandstrom R,
Li G,
Sandhu K,
Ruan Y,
Nielsen L,
Mattick J,
Stamatoyannopoulos J.
DNase I-hypersensitive exons colocalize with promoters and distal regulatory elements. Nat Genet 2013 Aug; 45(8):852-9.