期刊
GENOME RESEARCH
卷 23, 期 8, 页码 1295-1306出版社
COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
DOI: 10.1101/gr.149419.112
关键词
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资金
- CAREER grant from the National Science Foundation [DB1054964]
- Starr Cancer Consortium [I4-A411]
- LLS SCOR grant [7132-08]
- Institute for Computational Biomedicine, Weill Cornell Medical College
- Div Of Biological Infrastructure
- Direct For Biological Sciences [1054964] Funding Source: National Science Foundation
Genome-wide binding assays can determine where individual transcription factors bind in the genome. However, these factors rarely bind chromatin alone, but instead frequently bind to cis-regulatory elements (CREs) together with other factors thus forming protein complexes. Currently there are no integrative analytical approaches that can predict which complexes are formed on chromatin. Here, we describe a computational methodology to systematically capture protein complexes and infer their impact on gene expression. We applied our method to three human cell types, identified thousands of CREs, inferred known and undescribed complexes recruited to these CREs, and determined the role of the complexes as activators or repressors. Importantly, we found that the predicted complexes have a higher number of physical interactions between their members than expected by chance. Our work provides a mechanism for developing hypotheses about gene regulation via binding partners, and deciphering the interplay between combinatorial binding and gene expression.
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