Sabari, Benjamin R. and Dall’Agnese, Alessandra and Boija, Ann and Klein, Isaac A. and Coffey, Eliot L. and Shrinivas, Krishna and Abraham, Brian J. and Hannett, Nancy M. and Zamudio, Alicia V. and Manteiga, John C. and Li, Charles H. and Guo, Yang E. and Day, Daniel S. and Schuijers, Jurian and Vasile, Eliza and Malik, Sohail and Hnisz, Denes and Lee, Tong Ihn and Cisse, Ibrahim I. and Roeder, Robert G. and Sharp, Phillip A. and Chakraborty, Arup K. and Young, Richard A. (2018) Coactivator condensation at super-enhancers links phase separation and gene control. Science, 361 (6400). Art. No. eaar3958. ISSN 0036-8075. PMCID PMC6092193. doi:10.1126/science.aar3958. https://resolver.caltech.edu/CaltechAUTHORS:20201113-163228096
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Abstract
Super-enhancers (SEs) are clusters of enhancers that cooperatively assemble a high density of the transcriptional apparatus to drive robust expression of genes with prominent roles in cell identity. Here we demonstrate that the SE-enriched transcriptional coactivators BRD4 and MED1 form nuclear puncta at SEs that exhibit properties of liquid-like condensates and are disrupted by chemicals that perturb condensates. The intrinsically disordered regions (IDRs) of BRD4 and MED1 can form phase-separated droplets, and MED1-IDR droplets can compartmentalize and concentrate the transcription apparatus from nuclear extracts. These results support the idea that coactivators form phase-separated condensates at SEs that compartmentalize and concentrate the transcription apparatus, suggest a role for coactivator IDRs in this process, and offer insights into mechanisms involved in the control of key cell-identity genes.
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| Additional Information: | © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works http://www.sciencemag.org/about/science-licenses-journal-article-reuse. This is an article distributed under the terms of the Science Journals Default License. Received for publication November 4, 2017. Resubmitted April 9, 2018. Accepted for publication June 6, 2018. We thank W. Salmon of the W. M. Keck Microscopy Facility; D. Richardson and S. Terclavers of the Harvard Center for Biological Imaging; and T. Volkert, D. Reynolds, S. Mraz, and S. Gupta of the Whitehead Genome Technologies Core for technical assistance. We thank the Imaging Platform at the Broad Institute for assistance with CellProfiler. The work was supported by NIH grants GM123511 (R.A.Y.) and P01-CA042063 (P.A.S.), NSF grant PHY-1743900 (A.K.C., R.A.Y., and P.A.S.), Koch Institute Support (core) grant P30-CA14051 from the NCI (P.A.S.), Damon Runyon Cancer Research Foundation Fellowship 2309-17 (B.R.S.), Swedish Research Council Postdoctoral Fellowship VR 2017-00372 (A.B.), a Hope Funds for Cancer Research fellowship (B.J.A.), an NSF Graduate Research Fellowship (A.V.Z.), a Cancer Research Institute Irvington Fellowship (Y.E.G.), American Cancer Society New England Division Postdoctoral Fellowship PF-16-146-01-DMC (D.S.D.), and a NWO Rubicon Fellowship (J.S.). Author contributions: B.R.S., A.D., and R.A.Y. conceptualized and organized the project and wrote the manuscript. A.D., A.B., J.C.M., and Y.E.G. performed cell-imaging experiments and image analysis. I.A.K. and A.V.Z. generated endogenously tagged cell lines. B.R.S. and A.B. performed ChIP-seq. B.R.S. and E.L.C. performed in vitro droplet assays and optoIDR experiments. K.S. and B.J.A. developed and performed image analysis and produced visualizations. B.J.A. performed ChIP-seq analysis and produced visualizations. N.M.H. produced and purified recombinant proteins. A.V.Z. helped with biochemical experiments. C.H.L. performed protein amino acid analysis. D.S.D. performed ChIA-PET analysis and visualization. B.R.S., I.A.K., E.L.C., J.S., and A.V.Z. generated constructs. S.M. performed in vitro transcription assays. D.H., E.V., T.I.L., I.I.C., R.G.R., P.A.S., A.K.C., and R.A.Y. provided input into experimental design and interpretation. P.A.S., A.K.C., and R.A.Y. acquired funding for this study. R.A.Y. supervised the project with help from T.I.L. and A.K.C. All authors contributed to editing the manuscript. Competing interests: The Whitehead Institute filed a patent application based on this paper. R.A.Y. is a founder and shareholder of Syros Pharmaceuticals, Camp4 Therapeutics, and Omega Therapeutics. B.J.A. and T.I.L. are shareholders of Syros Pharmaceuticals, and T.I.L. is a consultant to Camp4 Therapeutics. All other authors declare no competing interests. Data and materials availability: Datasets generated in this study have been deposited in the Gene Expression Omnibus under accession number GSE112808. | ||||||||||||||||||||||||||||||||||||||||
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| Issue or Number: | 6400 | ||||||||||||||||||||||||||||||||||||||||
| PubMed Central ID: | PMC6092193 | ||||||||||||||||||||||||||||||||||||||||
| DOI: | 10.1126/science.aar3958 | ||||||||||||||||||||||||||||||||||||||||
| Record Number: | CaltechAUTHORS:20201113-163228096 | ||||||||||||||||||||||||||||||||||||||||
| Persistent URL: | https://resolver.caltech.edu/CaltechAUTHORS:20201113-163228096 | ||||||||||||||||||||||||||||||||||||||||
| Official Citation: | Coactivator condensation at super-enhancers links phase separation and gene control BY BENJAMIN R. SABARI, ALESSANDRA DALL’AGNESE, ANN BOIJA, ISAAC A. KLEIN, ELIOT L. COFFEY, KRISHNA SHRINIVAS, BRIAN J. ABRAHAM, NANCY M. HANNETT, ALICIA V. ZAMUDIO, JOHN C. MANTEIGA, CHARLES H. LI, YANG E. GUO, DANIEL S. DAY, JURIAN SCHUIJERS, ELIZA VASILE, SOHAIL MALIK, DENES HNISZ, TONG IHN LEE, IBRAHIM I. CISSE, ROBERT G. ROEDER, PHILLIP A. SHARP, ARUP K. CHAKRABORTY, RICHARD A. YOUNG Science 27 Jul 2018: Vol. 361, Issue 6400, eaar3958 DOI: 10.1126/science.aar3958 | ||||||||||||||||||||||||||||||||||||||||
| Usage Policy: | No commercial reproduction, distribution, display or performance rights in this work are provided. | ||||||||||||||||||||||||||||||||||||||||
| ID Code: | 106672 | ||||||||||||||||||||||||||||||||||||||||
| Collection: | CaltechAUTHORS | ||||||||||||||||||||||||||||||||||||||||
| Deposited By: | George Porter | ||||||||||||||||||||||||||||||||||||||||
| Deposited On: | 25 Nov 2020 20:24 | ||||||||||||||||||||||||||||||||||||||||
| Last Modified: | 16 Nov 2021 18:55 |
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