期刊
NUCLEIC ACIDS RESEARCH
卷 45, 期 20, 页码 11547-11558出版社
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkx784
关键词
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资金
- National Institutes of Health [R01GM126558, R21Al126308, R01AI121286, R21AI117687]
- Research Open Access Publishing (ROAAP) Fund of the University of Illinois at Chicago
- Chicago Biomedical Consortium
- Searle Funds at The Chicago Community Trust
Conformation capture technologies measure frequencies of interactions between chromatin regions. However, understanding gene-regulation require knowledge of detailed spatial structures of heterogeneous chromatin in cells. Here we describe the nC-SAC (n-Constrained-Self Avoiding Chromatin) method that transforms experimental interaction frequencies into 3D ensembles of chromatin chains. nC-SAC first distinguishes specific from non-specific interaction frequencies, then generates 3D chromatin ensembles using identified specific interactions as spatial constraints. Application to alpha-globin locus shows that these constraints (similar to 20%) drive the formation of similar to 99% all experimentally captured interactions, in which similar to 30% additional to the imposed constraints is found to be specific. Many novel specific spatial contacts not captured by experiments are also predicted. A subset, of which independent ChlA-PET data are available, is validated to be RNAPII-, CTCF-, and RAD21-mediated. Their positioning in the architectural context of imposed specific interactions from nC-SAC is highly important. Our results also suggest the presence of a many-body structural unit involving alpha-globin gene, its enhancers, and POL3RK gene for regulating the expression of alpha-globin in silent cells.
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