Voltar
Revisão Acesso aberto Revisado por pares
BIBTEX RIS

A Phase Separation Model for Transcriptional Control

2017; Cell Press; Volume: 169; Issue: 1 Linguagem: Inglês

10.1016/j.cell.2017.02.007

ISSN

1097-4172

Autores

Denes Hnisz, Krishna Shrinivas, Richard A. Young, Arup K. Chakraborty, Phillip A. Sharp,

Tópico(s)

RNA and protein synthesis mechanisms

Resumo

Phase-separated multi-molecular assemblies provide a general regulatory mechanism to compartmentalize biochemical reactions within cells. We propose that a phase separation model explains established and recently described features of transcriptional control. These features include the formation of super-enhancers, the sensitivity of super-enhancers to perturbation, the transcriptional bursting patterns of enhancers, and the ability of an enhancer to produce simultaneous activation at multiple genes. This model provides a conceptual framework to further explore principles of gene control in mammals. Phase-separated multi-molecular assemblies provide a general regulatory mechanism to compartmentalize biochemical reactions within cells. We propose that a phase separation model explains established and recently described features of transcriptional control. These features include the formation of super-enhancers, the sensitivity of super-enhancers to perturbation, the transcriptional bursting patterns of enhancers, and the ability of an enhancer to produce simultaneous activation at multiple genes. This model provides a conceptual framework to further explore principles of gene control in mammals. Recent studies of transcriptional regulation have revealed several puzzling observations that, as of yet, lack quantitative description, but the further understanding of which would likely afford new and valuable insights into gene control during development and disease. For example, although thousands of enhancer elements control the activity of thousands of genes in any given human cell type, several hundred clusters of enhancers, called super-enhancers (SEs), control genes that have especially prominent roles in cell-type-specific processes (ENCODE Project Consortium, 2012ENCODE Project ConsortiumAn integrated encyclopedia of DNA elements in the human genome.Nature. 2012; 489: 57-74Crossref PubMed Scopus (11031) Google Scholar, Hnisz et al., 2013Hnisz D. Abraham B.J. Lee T.I. Lau A. Saint-André V. Sigova A.A. Hoke H.A. Young R.A. Super-enhancers in the control of cell identity and disease.Cell. 2013; 155: 934-947Abstract Full Text Full Text PDF PubMed Scopus (2102) Google Scholar, Lovén et al., 2013Lovén J. Hoke H.A. Lin C.Y. Lau A. Orlando D.A. Vakoc C.R. Bradner J.E. Lee T.I. Young R.A. Selective inhibition of tumor oncogenes by disruption of super-enhancers.Cell. 2013; 153: 320-334Abstract Full Text Full Text PDF PubMed Scopus (1814) Google Scholar, Parker et al., 2013Parker S.C. Stitzel M.L. Taylor D.L. Orozco J.M. Erdos M.R. Akiyama J.A. van Bueren K.L. Chines P.S. Narisu N. Black B.L. et al.NISC Comparative Sequencing ProgramNational Institutes of Health Intramural Sequencing Center Comparative Sequencing Program AuthorsNISC Comparative Sequencing Program AuthorsChromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants.Proc. Natl. Acad. Sci. USA. 2013; 110: 17921-17926Crossref PubMed Scopus (462) Google Scholar, Kundaje et al., 2015Kundaje A. Meuleman W. Ernst J. Bilenky M. Yen A. Heravi-Moussavi A. Kheradpour P. Zhang Z. Wang J. Ziller M.J. et al.Roadmap Epigenomics ConsortiumIntegrative analysis of 111 reference human epigenomes.Nature. 2015; 518: 317-330Crossref PubMed Scopus (3578) Google Scholar, Whyte et al., 2013Whyte W.A. Orlando D.A. Hnisz D. Abraham B.J. Lin C.Y. Kagey M.H. Rahl P.B. Lee T.I. Young R.A. Master transcription factors and mediator establish super-enhancers at key cell identity genes.Cell. 2013; 153: 307-319Abstract Full Text Full Text PDF PubMed Scopus (2289) Google Scholar). Cancer cells acquire super-enhancers to drive expression of prominent oncogenes, so SEs play key roles in both development and disease (Chapuy et al., 2013Chapuy B. McKeown M.R. Lin C.Y. Monti S. Roemer M.G. Qi J. Rahl P.B. Sun H.H. Yeda K.T. Doench J.G. et al.Discovery and characterization of super-enhancer-associated dependencies in diffuse large B cell lymphoma.Cancer Cell. 2013; 24: 777-790Abstract Full Text Full Text PDF PubMed Scopus (521) Google Scholar, Lovén et al., 2013Lovén J. Hoke H.A. Lin C.Y. Lau A. Orlando D.A. Vakoc C.R. Bradner J.E. Lee T.I. Young R.A. Selective inhibition of tumor oncogenes by disruption of super-enhancers.Cell. 2013; 153: 320-334Abstract Full Text Full Text PDF PubMed Scopus (1814) Google Scholar). Super-enhancers are occupied by an unusually high density of interacting factors, are able to drive higher levels of transcription than typical enhancers, and are exceptionally vulnerable to perturbation of components commonly associated with most enhancers (Chapuy et al., 2013Chapuy B. McKeown M.R. Lin C.Y. Monti S. Roemer M.G. Qi J. Rahl P.B. Sun H.H. Yeda K.T. Doench J.G. et al.Discovery and characterization of super-enhancer-associated dependencies in diffuse large B cell lymphoma.Cancer Cell. 2013; 24: 777-790Abstract Full Text Full Text PDF PubMed Scopus (521) Google Scholar, Hnisz et al., 2013Hnisz D. Abraham B.J. Lee T.I. Lau A. Saint-André V. Sigova A.A. Hoke H.A. Young R.A. Super-enhancers in the control of cell identity and disease.Cell. 2013; 155: 934-947Abstract Full Text Full Text PDF PubMed Scopus (2102) Google Scholar, Lovén et al., 2013Lovén J. Hoke H.A. Lin C.Y. Lau A. Orlando D.A. Vakoc C.R. Bradner J.E. Lee T.I. Young R.A. Selective inhibition of tumor oncogenes by disruption of super-enhancers.Cell. 2013; 153: 320-334Abstract Full Text Full Text PDF PubMed Scopus (1814) Google Scholar, Whyte et al., 2013Whyte W.A. Orlando D.A. Hnisz D. Abraham B.J. Lin C.Y. Kagey M.H. Rahl P.B. Lee T.I. Young R.A. Master transcription factors and mediator establish super-enhancers at key cell identity genes.Cell. 2013; 153: 307-319Abstract Full Text Full Text PDF PubMed Scopus (2289) Google Scholar). Another puzzling observation that has emerged from recent studies is that a single enhancer is able to simultaneously activate multiple proximal genes (Fukaya et al., 2016Fukaya T. Lim B. Levine M. Enhancer control of transcriptional bursting.Cell. 2016; 166: 358-368Abstract Full Text Full Text PDF PubMed Scopus (360) Google Scholar). Enhancers physically contact the promoters of the genes they activate, and early studies using chromatin contact mapping techniques (e.g., at the β-globin locus) found that at any given time, enhancers activate only one of the several globin genes within the locus (Palstra et al., 2003Palstra R.J. Tolhuis B. Splinter E. Nijmeijer R. Grosveld F. de Laat W. The beta-globin nuclear compartment in development and erythroid differentiation.Nat. Genet. 2003; 35: 190-194Crossref PubMed Scopus (436) Google Scholar, Tolhuis et al., 2002Tolhuis B. Palstra R.J. Splinter E. Grosveld F. de Laat W. Looping and interaction between hypersensitive sites in the active beta-globin locus.Mol. Cell. 2002; 10: 1453-1465Abstract Full Text Full Text PDF PubMed Scopus (1052) Google Scholar). However, more recent work using quantitative imaging at a high temporal resolution revealed that enhancers typically activate genes in bursts, and that two gene promoters can exhibit synchronous bursting when activated by the same enhancer (Fukaya et al., 2016Fukaya T. Lim B. Levine M. Enhancer control of transcriptional bursting.Cell. 2016; 166: 358-368Abstract Full Text Full Text PDF PubMed Scopus (360) Google Scholar). Previous models of transcriptional control have provided important insights into principles of gene regulation. A key feature of most previous transcriptional control models is that the underlying regulatory interactions occur in a stepwise manner dictated by biochemical rules that are probabilistic in nature (Chen and Larson, 2016Chen H. Larson D.R. What have single-molecule studies taught us about gene expression?.Genes Dev. 2016; 30: 1796-1810Crossref PubMed Scopus (33) Google Scholar, Elowitz et al., 2002Elowitz M.B. Levine A.J. Siggia E.D. Swain P.S. Stochastic gene expression in a single cell.Science. 2002; 297: 1183-1186Crossref PubMed Scopus (3826) Google Scholar, Levine et al., 2014Levine M. Cattoglio C. Tjian R. Looping back to leap forward: transcription enters a new era.Cell. 2014; 157: 13-25Abstract Full Text Full Text PDF PubMed Scopus (324) Google Scholar, Orphanides and Reinberg, 2002Orphanides G. Reinberg D. A unified theory of gene expression.Cell. 2002; 108: 439-451Abstract Full Text Full Text PDF PubMed Scopus (704) Google Scholar, Raser and O’Shea, 2004Raser J.M. O’Shea E.K. Control of stochasticity in eukaryotic gene expression.Science. 2004; 304: 1811-1814Crossref PubMed Scopus (1112) Google Scholar, Spitz and Furlong, 2012Spitz F. Furlong E.E. Transcription factors: from enhancer binding to developmental control.Nat. Rev. Genet. 2012; 13: 613-626Crossref PubMed Scopus (1168) Google Scholar, Suter et al., 2011Suter D.M. Molina N. Gatfield D. Schneider K. Schibler U. Naef F. Mammalian genes are transcribed with widely different bursting kinetics.Science. 2011; 332: 472-474Crossref PubMed Scopus (596) Google Scholar, Zoller et al., 2015Zoller B. Nicolas D. Molina N. Naef F. Structure of silent transcription intervals and noise characteristics of mammalian genes.Mol. Syst. Biol. 2015; 11: 823Crossref PubMed Scopus (68) Google Scholar). Such kinetic models predict that gene activation on a single gene level is a stochastic, noisy process, and also provide insights into how multi-step regulatory processes can suppress intrinsic noise and result in bursting. These models do not shed light on the mechanisms underlying the formation, function, and properties of SEs or explain puzzles such as how two gene promoters exhibit synchronous bursting when activated by the same enhancer. In this perspective, we propose and explore a model that may explain the puzzles described above. This model is based on principles involving the phase separation of multi-molecular assemblies. Since the discovery of enhancers over 30 years ago, studies have attempted to describe functional properties of enhancers in a quantitative manner, and these efforts have mostly relied on the concept of cooperative interactions between enhancer components. Classically, enhancers have been defined as elements that can increase transcription from a target gene promoter when inserted in either orientation at various distances upstream or downstream of the promoter (Banerji et al., 1981Banerji J. Rusconi S. Schaffner W. Expression of a beta-globin gene is enhanced by remote SV40 DNA sequences.Cell. 1981; 27: 299-308Abstract Full Text PDF PubMed Scopus (916) Google Scholar, Benoist and Chambon, 1981Benoist C. Chambon P. In vivo sequence requirements of the SV40 early promotor region.Nature. 1981; 290: 304-310Crossref PubMed Scopus (539) Google Scholar, Gruss et al., 1981Gruss P. Dhar R. Khoury G. Simian virus 40 tandem repeated sequences as an element of the early promoter.Proc. Natl. Acad. Sci. USA. 1981; 78: 943-947Crossref PubMed Scopus (221) Google Scholar). Enhancers typically consist of hundreds of base-pairs of DNA and are bound by multiple transcription factor (TF) molecules in a cooperative manner (Bulger and Groudine, 2011Bulger M. Groudine M. Functional and mechanistic diversity of distal transcription enhancers.Cell. 2011; 144: 327-339Abstract Full Text Full Text PDF PubMed Scopus (596) Google Scholar, Levine et al., 2014Levine M. Cattoglio C. Tjian R. Looping back to leap forward: transcription enters a new era.Cell. 2014; 157: 13-25Abstract Full Text Full Text PDF PubMed Scopus (324) Google Scholar, Malik and Roeder, 2010Malik S. Roeder R.G. The metazoan Mediator co-activator complex as an integrative hub for transcriptional regulation.Nat. Rev. Genet. 2010; 11: 761-772Crossref PubMed Scopus (532) Google Scholar, Ong and Corces, 2011Ong C.T. Corces V.G. Enhancer function: new insights into the regulation of tissue-specific gene expression.Nat. Rev. Genet. 2011; 12: 283-293Crossref PubMed Scopus (605) Google Scholar, Spitz and Furlong, 2012Spitz F. Furlong E.E. Transcription factors: from enhancer binding to developmental control.Nat. Rev. Genet. 2012; 13: 613-626Crossref PubMed Scopus (1168) Google Scholar). Classically, cooperative binding describes the phenomenon that the binding of one TF molecule to DNA impacts the binding of another TF molecule (Figure 1A) (Carey, 1998Carey M. The enhanceosome and transcriptional synergy.Cell. 1998; 92: 5-8Abstract Full Text Full Text PDF PubMed Scopus (453) Google Scholar, Kim and Maniatis, 1997Kim T.K. Maniatis T. The mechanism of transcriptional synergy of an in vitro assembled interferon-beta enhanceosome.Mol. Cell. 1997; 1: 119-129Abstract Full Text Full Text PDF PubMed Scopus (298) Google Scholar, Thanos and Maniatis, 1995Thanos D. Maniatis T. Virus induction of human IFN beta gene expression requires the assembly of an enhanceosome.Cell. 1995; 83: 1091-1100Abstract Full Text PDF PubMed Scopus (852) Google Scholar, Tjian and Maniatis, 1994Tjian R. Maniatis T. Transcriptional activation: a complex puzzle with few easy pieces.Cell. 1994; 77: 5-8Abstract Full Text PDF PubMed Scopus (955) Google Scholar). Cooperative binding of transcription factors at enhancers has been proposed to be due to the effects of TFs on DNA bending (Falvo et al., 1995Falvo J.V. Thanos D. Maniatis T. Reversal of intrinsic DNA bends in the IFN beta gene enhancer by transcription factors and the architectural protein HMG I(Y).Cell. 1995; 83: 1101-1111Abstract Full Text PDF PubMed Scopus (277) Google Scholar), interactions between TFs (Johnson et al., 1979Johnson A.D. Meyer B.J. Ptashne M. Interactions between DNA-bound repressors govern regulation by the lambda phage repressor.Proc. Natl. Acad. Sci. USA. 1979; 76: 5061-5065Crossref PubMed Scopus (272) Google Scholar), and combinatorial recruitment of large cofactor complexes by TFs (Merika et al., 1998Merika M. Williams A.J. Chen G. Collins T. Thanos D. Recruitment of CBP/p300 by the IFN beta enhanceosome is required for synergistic activation of transcription.Mol. Cell. 1998; 1: 277-287Abstract Full Text Full Text PDF PubMed Scopus (365) Google Scholar). Several hundred clusters of enhancers, called super-enhancers (SEs), control genes that have especially prominent roles in cell-type-specific processes (Hnisz et al., 2013Hnisz D. Abraham B.J. Lee T.I. Lau A. Saint-André V. Sigova A.A. Hoke H.A. Young R.A. Super-enhancers in the control of cell identity and disease.Cell. 2013; 155: 934-947Abstract Full Text Full Text PDF PubMed Scopus (2102) Google Scholar, Whyte et al., 2013Whyte W.A. Orlando D.A. Hnisz D. Abraham B.J. Lin C.Y. Kagey M.H. Rahl P.B. Lee T.I. Young R.A. Master transcription factors and mediator establish super-enhancers at key cell identity genes.Cell. 2013; 153: 307-319Abstract Full Text Full Text PDF PubMed Scopus (2289) Google Scholar). Three key features of SEs indicate that cooperative properties are especially important for their formation and function: (1) SEs are occupied by an unusually high density of interacting factors; (2) SEs can be formed by a single nucleation event; and (3) SEs are exceptionally vulnerable to perturbation of some components commonly associated with most enhancers. SEs are occupied by an unusually high density of enhancer-associated factors, including transcription factors, co-factors, chromatin regulators, RNA polymerase II, and non-coding RNA (Hnisz et al., 2013Hnisz D. Abraham B.J. Lee T.I. Lau A. Saint-André V. Sigova A.A. Hoke H.A. Young R.A. Super-enhancers in the control of cell identity and disease.Cell. 2013; 155: 934-947Abstract Full Text Full Text PDF PubMed Scopus (2102) Google Scholar). The non-coding RNA (enhancer RNA or eRNA), produced by divergent transcription at transcription factor binding sites within SEs (Hah et al., 2015Hah N. Benner C. Chong L.W. Yu R.T. Downes M. Evans R.M. Inflammation-sensitive super enhancers form domains of coordinately regulated enhancer RNAs.Proc. Natl. Acad. Sci. USA. 2015; 112: E297-E302Crossref PubMed Scopus (111) Google Scholar, Sigova et al., 2013Sigova A.A. Mullen A.C. Molinie B. Gupta S. Orlando D.A. Guenther M.G. Almada A.E. Lin C. Sharp P.A. Giallourakis C.C. Young R.A. Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells.Proc. Natl. Acad. Sci. USA. 2013; 110: 2876-2881Crossref PubMed Scopus (342) Google Scholar), can contribute to enhancer activity and the expression of the nearby gene in cis (Dimitrova et al., 2014Dimitrova N. Zamudio J.R. Jong R.M. Soukup D. Resnick R. Sarma K. Ward A.J. Raj A. Lee J.T. Sharp P.A. Jacks T. LincRNA-p21 activates p21 in cis to promote Polycomb target gene expression and to enforce the G1/S checkpoint.Mol. Cell. 2014; 54: 777-790Abstract Full Text Full Text PDF PubMed Scopus (331) Google Scholar, Engreitz et al., 2016Engreitz J.M. Haines J.E. Perez E.M. Munson G. Chen J. Kane M. McDonel P.E. Guttman M. Lander E.S. Local regulation of gene expression by lncRNA promoters, transcription and splicing.Nature. 2016; 539: 452-455Crossref PubMed Scopus (751) Google Scholar, Lai et al., 2013Lai F. Orom U.A. Cesaroni M. Beringer M. Taatjes D.J. Blobel G.A. Shiekhattar R. Activating RNAs associate with mediator to enhance chromatin architecture and transcription.Nature. 2013; 494: 497-501Crossref PubMed Scopus (643) Google Scholar, Pefanis et al., 2015Pefanis E. Wang J. Rothschild G. Lim J. Kazadi D. Sun J. Federation A. Chao J. Elliott O. Liu Z.P. et al.RNA exosome-regulated long non-coding RNA transcription controls super-enhancer activity.Cell. 2015; 161: 774-789Abstract Full Text Full Text PDF PubMed Scopus (293) Google Scholar). The density of the protein factors and eRNAs at SEs has been estimated to be approximately 10-fold the density of the same set of components at typical enhancers in the genome (Figure 1B) (Hnisz et al., 2013Hnisz D. Abraham B.J. Lee T.I. Lau A. Saint-André V. Sigova A.A. Hoke H.A. Young R.A. Super-enhancers in the control of cell identity and disease.Cell. 2013; 155: 934-947Abstract Full Text Full Text PDF PubMed Scopus (2102) Google Scholar, Lovén et al., 2013Lovén J. Hoke H.A. Lin C.Y. Lau A. Orlando D.A. Vakoc C.R. Bradner J.E. Lee T.I. Young R.A. Selective inhibition of tumor oncogenes by disruption of super-enhancers.Cell. 2013; 153: 320-334Abstract Full Text Full Text PDF PubMed Scopus (1814) Google Scholar, Whyte et al., 2013Whyte W.A. Orlando D.A. Hnisz D. Abraham B.J. Lin C.Y. Kagey M.H. Rahl P.B. Lee T.I. Young R.A. Master transcription factors and mediator establish super-enhancers at key cell identity genes.Cell. 2013; 153: 307-319Abstract Full Text Full Text PDF PubMed Scopus (2289) Google Scholar). Chromatin contact mapping methods indicate that the clusters of enhancers within SEs are in close physical contact with one another and with the promoter region of the gene they activate (Figure 1C) (Dowen et al., 2014Dowen J.M. Fan Z.P. Hnisz D. Ren G. Abraham B.J. Zhang L.N. Weintraub A.S. Schuijers J. Lee T.I. Zhao K. Young R.A. Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes.Cell. 2014; 159: 374-387Abstract Full Text Full Text PDF PubMed Scopus (579) Google Scholar, Hnisz et al., 2016Hnisz D. Weintraub A.S. Day D.S. Valton A.L. Bak R.O. Li C.H. Goldmann J. Lajoie B.R. Fan Z.P. Sigova A.A. et al.Activation of proto-oncogenes by disruption of chromosome neighborhoods.Science. 2016; 351: 1454-1458Crossref PubMed Scopus (578) Google Scholar, Ji et al., 2016Ji X. Dadon D.B. Powell B.E. Fan Z.P. Borges-Rivera D. Shachar S. Weintraub A.S. Hnisz D. Pegoraro G. Lee T.I. et al.3D chromosome regulatory landscape of human pluripotent cells.Cell Stem Cell. 2016; 18: 262-275Abstract Full Text Full Text PDF PubMed Scopus (254) Google Scholar, Kieffer-Kwon et al., 2013Kieffer-Kwon K.R. Tang Z. Mathe E. Qian J. Sung M.H. Li G. Resch W. Baek S. Pruett N. Grøntved L. et al.Interactome maps of mouse gene regulatory domains reveal basic principles of transcriptional regulation.Cell. 2013; 155: 1507-1520Abstract Full Text Full Text PDF PubMed Scopus (244) Google Scholar). SEs can be formed as a consequence of introducing a single transcription factor binding site into a region of DNA that has the potential to bind additional factors. In T cell leukemias, a small (2–12 bp) mono-allelic insertion nucleates the formation of an entire SE by creating a binding site for the master transcription factor MYB, leading to the recruitment of additional transcriptional regulators to adjacent binding sites and assembly of a host of factors spread over an 8-kb domain whose features are typical of a SE (Mansour et al., 2014Mansour M.R. Abraham B.J. Anders L. Berezovskaya A. Gutierrez A. Durbin A.D. Etchin J. Lawton L. Sallan S.E. Silverman L.B. et al.Oncogene regulation. An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element.Science. 2014; 346: 1373-1377Crossref PubMed Scopus (514) Google Scholar). Inflammatory stimulation also leads to rapid formation of SEs in endothelial cells; here again, the formation of a SE is apparently nucleated by a single binding event of a transcription factor responsive to inflammatory stimulation (Brown et al., 2014Brown J.D. Lin C.Y. Duan Q. Griffin G. Federation A.J. Paranal R.M. Bair S. Newton G. Lichtman A.H. Kung A.L. et al.NF-κB directs dynamic super enhancer formation in inflammation and atherogenesis.Mol. Cell. 2014; 56: 219-231Abstract Full Text Full Text PDF PubMed Scopus (409) Google Scholar). Entire super-enhancers spanning tens of thousands of base pairs can collapse as a unit when their co-factors are perturbed, and genetic deletion of constituent enhancers within an SE can compromise the function of other constituents. For example, the co-activator BRD4 binds acetylated chromatin at SEs, typical enhancers and promoters, but SEs are far more sensitive to drugs blocking the binding of BRD4 to acetylated chromatin (Chapuy et al., 2013Chapuy B. McKeown M.R. Lin C.Y. Monti S. Roemer M.G. Qi J. Rahl P.B. Sun H.H. Yeda K.T. Doench J.G. et al.Discovery and characterization of super-enhancer-associated dependencies in diffuse large B cell lymphoma.Cancer Cell. 2013; 24: 777-790Abstract Full Text Full Text PDF PubMed Scopus (521) Google Scholar, Lovén et al., 2013Lovén J. Hoke H.A. Lin C.Y. Lau A. Orlando D.A. Vakoc C.R. Bradner J.E. Lee T.I. Young R.A. Selective inhibition of tumor oncogenes by disruption of super-enhancers.Cell. 2013; 153: 320-334Abstract Full Text Full Text PDF PubMed Scopus (1814) Google Scholar). A similar hypersensitivity of SEs to inhibition of the cyclin-dependent kinase CDK7 has also been observed in multiple studies (Chipumuro et al., 2014Chipumuro E. Marco E. Christensen C.L. Kwiatkowski N. Zhang T. Hatheway C.M. Abraham B.J. Sharma B. Yeung C. Altabef A. et al.CDK7 inhibition suppresses super-enhancer-linked oncogenic transcription in MYCN-driven cancer.Cell. 2014; 159: 1126-1139Abstract Full Text Full Text PDF PubMed Scopus (401) Google Scholar, Kwiatkowski et al., 2014Kwiatkowski N. Zhang T. Rahl P.B. Abraham B.J. Reddy J. Ficarro S.B. Dastur A. Amzallag A. Ramaswamy S. Tesar B. et al.Targeting transcription regulation in cancer with a covalent CDK7 inhibitor.Nature. 2014; 511: 616-620Crossref PubMed Scopus (536) Google Scholar, Wang et al., 2015Wang Y. Zhang T. Kwiatkowski N. Abraham B.J. Lee T.I. Xie S. Yuzugullu H. Von T. Li H. Lin Z. et al.CDK7-dependent transcriptional addiction in triple-negative breast cancer.Cell. 2015; 163: 174-186Abstract Full Text Full Text PDF PubMed Scopus (276) Google Scholar). This kinase is critical for initiation of transcription by RNA polymerase II (RNA Pol II) and phosphorylates its repetitive C-terminal domain (CTD) (Larochelle et al., 2012Larochelle S. Amat R. Glover-Cutter K. Sansó M. Zhang C. Allen J.J. Shokat K.M. Bentley D.L. Fisher R.P. Cyclin-dependent kinase control of the initiation-to-elongation switch of RNA polymerase II.Nat. Struct. Mol. Biol. 2012; 19: 1108-1115Crossref PubMed Scopus (259) Google Scholar). Furthermore, genetic deletion of constituent enhancers within SEs can compromise the activities of other constituents within the super-enhancer (Hnisz et al., 2015Hnisz D. Schuijers J. Lin C.Y. Weintraub A.S. Abraham B.J. Lee T.I. Bradner J.E. Young R.A. Convergence of developmental and oncogenic signaling pathways at transcriptional super-enhancers.Mol. Cell. 2015; 58: 362-370Abstract Full Text Full Text PDF PubMed Scopus (290) Google Scholar, Jiang et al., 2016Jiang T. Raviram R. Snetkova V. Rocha P.P. Proudhon C. Badri S. Bonneau R. Skok J.A. Kluger Y. Identification of multi-loci hubs from 4C-seq demonstrates the functional importance of simultaneous interactions.Nucleic Acids Res. 2016; 44: 8714-8725Crossref PubMed Scopus (29) Google Scholar, Proudhon et al., 2016Proudhon C. Snetkova V. Raviram R. Lobry C. Badri S. Jiang T. Hao B. Trimarchi T. Kluger Y. Aifantis I. et al.Active and Inactive Enhancers Cooperate to Exert Localized and Long-Range Control of Gene Regulation.Cell Rep. 2016; 15: 2159-2169Abstract Full Text Full Text PDF PubMed Scopus (25) Google Scholar, Shin et al., 2016Shin H.Y. Willi M. Yoo K.H. Zeng X. Wang C. Metser G. Hennighausen L. Hierarchy within the mammary STAT5-driven Wap super-enhancer.Nat. Genet. 2016; 48: 904-911Crossref PubMed Scopus (152) Google Scholar), and can lead to the collapse of an entire super-enhancer (Mansour et al., 2014Mansour M.R. Abraham B.J. Anders L. Berezovskaya A. Gutierrez A. Durbin A.D. Etchin J. Lawton L. Sallan S.E. Silverman L.B. et al.Oncogene regulation. An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element.Science. 2014; 346: 1373-1377Crossref PubMed Scopus (514) Google Scholar), although this interdependence of constituent enhancers is less apparent for some developmentally regulated super-enhancers (Hay et al., 2016Hay D. Hughes J.R. Babbs C. Davies J.O. Graham B.J. Hanssen L.L. Kassouf M.T. Oudelaar A.M. Sharpe J.A. Suciu M.C. et al.Genetic dissection of the α-globin super-enhancer in vivo.Nat. Genet. 2016; 48: 895-903Crossref PubMed Scopus (208) Google Scholar). In summary, several lines of evidence indicate that the formation and function of SEs involves cooperative processes that bring many constituent enhancers and their bound factors into close spatial proximity. High densities of proteins and nucleic acids—and cooperative interactions among these molecules—have been implicated in the formation of membraneless organelles, called cellular bodies, in eukaryotic cells (Banjade et al., 2015Banjade S. Wu Q. Mittal A. Peeples W.B. Pappu R.V. Rosen M.K. Conserved interdomain linker promotes phase separation of the multivalent adaptor protein Nck.Proc. Natl. Acad. Sci. USA. 2015; 112: E6426-E6435Crossref PubMed Scopus (108) Google Scholar, Bergeron-Sandoval et al., 2016Bergeron-Sandoval L.P. Safaee N. Michnick S.W. Mechanisms and consequences of macromolecular phase separation.Cell. 2016; 165: 1067-1079Abstract Full Text Full Text PDF PubMed Scopus (202) Google Scholar, Brangwynne et al., 2009Brangwynne C.P. Eckmann C.R. Courson D.S. Rybarska A. Hoege C. Gharakhani J. Jülicher F. Hyman A.A. Germline P granules are liquid droplets that localize by controlled dissolution/condensation.Science. 2009; 324: 1729-1732Crossref PubMed Scopus (1517) Google Scholar). Below, we first describe features of the formation of cellular bodies, and then develop a model of super-enhancer formation and function that exploits related concepts. Eukaryotic cells contain membraneless organelles, called cellular bodies, which play essential roles in compartmentalizing essential biochemical reactions within cells. These bodies are formed by phase separation mediated by cooperative interactions between multivalent molecules (Banani et al., 2017Banani S.F. Lee H.O. Hyman A.A. Rosen M.K. Biomolecular condensates: organizers of cellular biochemistry.Nat. Rev. Mol. Cell Bio. 2017; (Published online February 22, 2017)https://doi.org/10.1038/nrm.2017.7Crossref PubMed Scopus (2219) Google Scholar, Banjade et al., 2015Banjade S. Wu Q. Mittal A. Peeples W.B. Pappu R.V. Rosen M.K. Conserved interdomain linker promotes phase separation of the multivalent adaptor protein Nck.Proc. Natl. Acad. Sci. USA. 2015; 112: E6426-E6435Crossref PubMed Scopus (108) Google Scholar, Bergeron-Sandoval et al., 2016Bergeron-Sandoval L.P. Safaee N. Michnick S.W. Mechanisms and consequences of macromolecular phase separation.Cell. 2016; 165: 1067-1079Abstract Full Text Full Text PDF PubMed Scopus (202) Google Scholar, Brangwynne et al., 2009Brangwynne C.P. Eckmann C.R. Courson D.S. Rybarska A. Hoege C. Gharakhani J. Jülicher F. Hyman A.A. Germline P granules are liquid droplets that localize by controlled dissolution/condensation.Science. 2009; 324: 1729-1732Crossref PubMed Scopus (1517) Google Scholar). Examples of such organelles in the nucleus include nucleoli, which are sites of rRNA biogenesis; Cajal bodies, which serve as an assembly site for small nuclear RNPs; and nuclear speckles, which are storage compartments for mRNA splicing factors (Mao et al., 2011Mao Y.S. Zhang B. Spector D.L. Biogenesis and function of nuclear bodies.Trends Genet. 2011; 27: 295-306Abstract Full Text Full Text PDF PubMed Scopus (479) Google Scholar, Zhu and Brangwynne, 2015Zhu L. Brangwynne C.P. Nuclear bodies: the emerging biophysics of nucleoplasmic phases.Curr. Opin. Cell Biol. 2015; 34: 23-30Crossref PubMed Scopus (174) Google Scholar). These organelles exhibit properties of liquid droplets; for example, they can undergo fission and fusion, and hence their formation has been described as mediated by liquid-liquid phase separation. Mixtures of purified RNA and RNA-binding proteins form these types of phase-separated bodies in vitro (Berry et al., 2015Berry J. Weber S.C. Vaidya N. Haataja M. Brangwynne C.P. RNA transcription modulates phase transition-driven nuclear body assembly.Proc. Natl. Acad. Sci. USA. 2015; 112: E5237-E5245Crossref PubMed Scopus (287) Google Scholar, Feric et al., 201

Referência(s)