Journal article
DNase I-hypersensitive exons colocalize with promoters and distal regulatory elements
TR Mercer, SL Edwards, MB Clark, SJ Neph, H Wang, AB Stergachis, S John, R Sandstrom, G Li, KS Sandhu, Y Ruan, LK Nielsen, JS Mattick, JA Stamatoyannopoulos
Nature Genetics | NATURE PUBLISHING GROUP | Published : 2013
DOI: 10.1038/ng.2677
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 ..
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Awarded by National Human Genome Research Institute
Funding Acknowledgements
The authors would like to thank the following funding sources: the Australian National Health and Medical Research Council (Australia Fellowships 631668 to J.S.M., T. R. M. and M. B. C. and 631381 and 1021731 to S. L. E.); the Queensland State Government (National and International Research Alliance Program to L.K.N.); the National Breast Cancer Foundation Australia (to S. L. E.); the National Human Genome Research Institute (NHGRI; ENCODE grant HG004456 to Y.R., G. L. and K. S. S.); and the US National Institutes of Health (NHGRI ENCODE grants U54HG004592 and U54HG007599 to J.A.S.).