Combinatorial Patterning of Chromatin Regulators Uncovered by Genome-wide Location Analysis in Human Cells
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Ram-2011-Combinatorial Patter.pdf
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Author(s)
Ram, Oren
Goren, Alon
Amit, Ido
Shoresh, Noam
Yosef, Nir
Ernst, Jason
Kellis, Manolis
Issner, Robbyn
Durham, Timothy
Zhang, Xiaolan
Date Issued
December 2011
Journal
Cell
Publisher
Elsevier
Citation
Ram, Oren, Alon Goren, Ido Amit, Noam Shoresh, Nir Yosef, Jason Ernst, Manolis Kellis, et al. “Combinatorial Patterning of Chromatin Regulators Uncovered by Genome-Wide Location Analysis in Human Cells.” Cell 147, no. 7 (December 2011): 1628–1639. © 2011 Elsevier Inc.
Version
Final published version
Abstract
Hundreds of chromatin regulators (CRs) control chromatin structure and function by catalyzing and binding histone modifications, yet the rules governing these key processes remain obscure. Here, we present a systematic approach to infer CR function. We developed ChIP-string, a meso-scale assay that combines chromatin immunoprecipitation with a signature readout of 487 representative loci. We applied ChIP-string to screen 145 antibodies, thereby identifying effective reagents, which we used to map the genome-wide binding of 29 CRs in two cell types. We found that specific combinations of CRs colocalize in characteristic patterns at distinct chromatin environments, at genes of coherent functions, and at distal regulatory elements. When comparing between cell types, CRs redistribute to different loci but maintain their modular and combinatorial associations. Our work provides a multiplex method that substantially enhances the ability to monitor CR binding, presents a large resource of CR maps, and reveals common principles for combinatorial CR function.
MIT Department
Harvard University--MIT Division of Health Sciences and Technology
Lincoln Laboratory
Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory
Massachusetts Institute of Technology. Department of Biology
Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science
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Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use.
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DOI of Published Version
https://doi.org/10.1016/j.cell.2011.09.057
