Literature DB >> 28340338

A Phase Separation Model for Transcriptional Control.

Denes Hnisz1, Krishna Shrinivas2, Richard A Young3, Arup K Chakraborty4, Phillip A Sharp5.   

Abstract

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.
Copyright © 2017 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  bursting; co-operativity; enhancer; gene control; nuclear body; phase separation; super-enhancer; transcription; transcriptional burst

Mesh:

Substances:

Year:  2017        PMID: 28340338      PMCID: PMC5432200          DOI: 10.1016/j.cell.2017.02.007

Source DB:  PubMed          Journal:  Cell        ISSN: 0092-8674            Impact factor:   41.582


  78 in total

1.  Super-enhancers in the control of cell identity and disease.

Authors:  Denes Hnisz; Brian J Abraham; Tong Ihn Lee; Ashley Lau; Violaine Saint-André; Alla A Sigova; Heather A Hoke; Richard A Young
Journal:  Cell       Date:  2013-10-10       Impact factor: 41.582

2.  Targeting transcriptional addictions in small cell lung cancer with a covalent CDK7 inhibitor.

Authors:  Camilla L Christensen; Nicholas Kwiatkowski; Brian J Abraham; Julian Carretero; Fatima Al-Shahrour; Tinghu Zhang; Edmond Chipumuro; Grit S Herter-Sprie; Esra A Akbay; Abigail Altabef; Jianming Zhang; Takeshi Shimamura; Marzia Capelletti; Jakob B Reibel; Jillian D Cavanaugh; Peng Gao; Yan Liu; Signe R Michaelsen; Hans S Poulsen; Amir R Aref; David A Barbie; James E Bradner; Rani E George; Nathanael S Gray; Richard A Young; Kwok-Kin Wong
Journal:  Cancer Cell       Date:  2014-12-08       Impact factor: 31.743

Review 3.  Nature, nurture, or chance: stochastic gene expression and its consequences.

Authors:  Arjun Raj; Alexander van Oudenaarden
Journal:  Cell       Date:  2008-10-17       Impact factor: 41.582

4.  Selective inhibition of tumor oncogenes by disruption of super-enhancers.

Authors:  Jakob Lovén; Heather A Hoke; Charles Y Lin; Ashley Lau; David A Orlando; Christopher R Vakoc; James E Bradner; Tong Ihn Lee; Richard A Young
Journal:  Cell       Date:  2013-04-11       Impact factor: 41.582

5.  Enhancer Control of Transcriptional Bursting.

Authors:  Takashi Fukaya; Bomyi Lim; Michael Levine
Journal:  Cell       Date:  2016-06-09       Impact factor: 41.582

6.  Phosphorylation-regulated binding of RNA polymerase II to fibrous polymers of low-complexity domains.

Authors:  Ilmin Kwon; Masato Kato; Siheng Xiang; Leeju Wu; Pano Theodoropoulos; Hamid Mirzaei; Tina Han; Shanhai Xie; Jeffry L Corden; Steven L McKnight
Journal:  Cell       Date:  2013-11-21       Impact factor: 41.582

Review 7.  Looping back to leap forward: transcription enters a new era.

Authors:  Michael Levine; Claudia Cattoglio; Robert Tjian
Journal:  Cell       Date:  2014-03-27       Impact factor: 41.582

8.  Identification of multi-loci hubs from 4C-seq demonstrates the functional importance of simultaneous interactions.

Authors:  Tingting Jiang; Ramya Raviram; Valentina Snetkova; Pedro P Rocha; Charlotte Proudhon; Sana Badri; Richard Bonneau; Jane A Skok; Yuval Kluger
Journal:  Nucleic Acids Res       Date:  2016-07-20       Impact factor: 16.971

9.  Integrative analysis of 111 reference human epigenomes.

Authors:  Anshul Kundaje; Wouter Meuleman; Jason Ernst; Misha Bilenky; Angela Yen; Alireza Heravi-Moussavi; Pouya Kheradpour; Zhizhuo Zhang; Jianrong Wang; Michael J Ziller; Viren Amin; John W Whitaker; Matthew D Schultz; Lucas D Ward; Abhishek Sarkar; Gerald Quon; Richard S Sandstrom; Matthew L Eaton; Yi-Chieh Wu; Andreas R Pfenning; Xinchen Wang; Melina Claussnitzer; Yaping Liu; Cristian Coarfa; R Alan Harris; Noam Shoresh; Charles B Epstein; Elizabeta Gjoneska; Danny Leung; Wei Xie; R David Hawkins; Ryan Lister; Chibo Hong; Philippe Gascard; Andrew J Mungall; Richard Moore; Eric Chuah; Angela Tam; Theresa K Canfield; R Scott Hansen; Rajinder Kaul; Peter J Sabo; Mukul S Bansal; Annaick Carles; Jesse R Dixon; Kai-How Farh; Soheil Feizi; Rosa Karlic; Ah-Ram Kim; Ashwinikumar Kulkarni; Daofeng Li; Rebecca Lowdon; GiNell Elliott; Tim R Mercer; Shane J Neph; Vitor Onuchic; Paz Polak; Nisha Rajagopal; Pradipta Ray; Richard C Sallari; Kyle T Siebenthall; Nicholas A Sinnott-Armstrong; Michael Stevens; Robert E Thurman; Jie Wu; Bo Zhang; Xin Zhou; Arthur E Beaudet; Laurie A Boyer; Philip L De Jager; Peggy J Farnham; Susan J Fisher; David Haussler; Steven J M Jones; Wei Li; Marco A Marra; Michael T McManus; Shamil Sunyaev; James A Thomson; Thea D Tlsty; Li-Huei Tsai; Wei Wang; Robert A Waterland; Michael Q Zhang; Lisa H Chadwick; Bradley E Bernstein; Joseph F Costello; Joseph R Ecker; Martin Hirst; Alexander Meissner; Aleksandar Milosavljevic; Bing Ren; John A Stamatoyannopoulos; Ting Wang; Manolis Kellis
Journal:  Nature       Date:  2015-02-19       Impact factor: 69.504

10.  Response and resistance to BET bromodomain inhibitors in triple-negative breast cancer.

Authors:  Shaokun Shu; Charles Y Lin; Housheng Hansen He; Robert M Witwicki; Doris P Tabassum; Justin M Roberts; Michalina Janiszewska; Sung Jin Huh; Yi Liang; Jeremy Ryan; Ernest Doherty; Hisham Mohammed; Hao Guo; Daniel G Stover; Muhammad B Ekram; Jonathan Brown; Clive D'Santos; Ian E Krop; Deborah Dillon; Michael McKeown; Christopher Ott; Jun Qi; Min Ni; Prakash K Rao; Melissa Duarte; Shwu-Yuan Wu; Cheng-Ming Chiang; Lars Anders; Richard A Young; Eric Winer; Antony Letai; William T Barry; Jason S Carroll; Henry Long; Myles Brown; X Shirley Liu; Clifford A Meyer; James E Bradner; Kornelia Polyak
Journal:  Nature       Date:  2016-01-06       Impact factor: 49.962

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  527 in total

1.  Robust Hi-C Maps of Enhancer-Promoter Interactions Reveal the Function of Non-coding Genome in Neural Development and Diseases.

Authors:  Leina Lu; Xiaoxiao Liu; Wei-Kai Huang; Paola Giusti-Rodríguez; Jian Cui; Shanshan Zhang; Wanying Xu; Zhexing Wen; Shufeng Ma; Jonathan D Rosen; Zheng Xu; Cynthia F Bartels; Riki Kawaguchi; Ming Hu; Peter C Scacheri; Zhili Rong; Yun Li; Patrick F Sullivan; Hongjun Song; Guo-Li Ming; Yan Li; Fulai Jin
Journal:  Mol Cell       Date:  2020-06-26       Impact factor: 17.970

2.  Liquid Nuclear Condensates Mechanically Sense and Restructure the Genome.

Authors:  Yongdae Shin; Yi-Che Chang; Daniel S W Lee; Joel Berry; David W Sanders; Pierre Ronceray; Ned S Wingreen; Mikko Haataja; Clifford P Brangwynne
Journal:  Cell       Date:  2018-11-29       Impact factor: 41.582

3.  Mapping Local and Global Liquid Phase Behavior in Living Cells Using Photo-Oligomerizable Seeds.

Authors:  Dan Bracha; Mackenzie T Walls; Ming-Tzo Wei; Lian Zhu; Martin Kurian; José L Avalos; Jared E Toettcher; Clifford P Brangwynne
Journal:  Cell       Date:  2018-11-29       Impact factor: 41.582

Review 4.  Phase Separation and Transcription Regulation: Are Super-Enhancers and Locus Control Regions Primary Sites of Transcription Complex Assembly?

Authors:  Aishwarya Gurumurthy; Yong Shen; Eliot M Gunn; Jörg Bungert
Journal:  Bioessays       Date:  2018-11-30       Impact factor: 4.345

Review 5.  Two major mechanisms of chromosome organization.

Authors:  Leonid A Mirny; Maxim Imakaev; Nezar Abdennur
Journal:  Curr Opin Cell Biol       Date:  2019-06-20       Impact factor: 8.382

6.  A Caenorhabditis elegans protein with a PRDM9-like SET domain localizes to chromatin-associated foci and promotes spermatocyte gene expression, sperm production and fertility.

Authors:  Christoph G Engert; Rita Droste; Alexander van Oudenaarden; H Robert Horvitz
Journal:  PLoS Genet       Date:  2018-04-27       Impact factor: 5.917

7.  The Energetics and Physiological Impact of Cohesin Extrusion.

Authors:  Laura Vian; Aleksandra Pękowska; Suhas S P Rao; Kyong-Rim Kieffer-Kwon; Seolkyoung Jung; Laura Baranello; Su-Chen Huang; Laila El Khattabi; Marei Dose; Nathanael Pruett; Adrian L Sanborn; Andres Canela; Yaakov Maman; Anna Oksanen; Wolfgang Resch; Xingwang Li; Byoungkoo Lee; Alexander L Kovalchuk; Zhonghui Tang; Steevenson Nelson; Michele Di Pierro; Ryan R Cheng; Ido Machol; Brian Glenn St Hilaire; Neva C Durand; Muhammad S Shamim; Elena K Stamenova; José N Onuchic; Yijun Ruan; Andre Nussenzweig; David Levens; Erez Lieberman Aiden; Rafael Casellas
Journal:  Cell       Date:  2018-04-26       Impact factor: 41.582

Review 8.  Evolving methodologies and concepts in 4D nucleome research.

Authors:  Thomas M Sparks; Izabela Harabula; Ana Pombo
Journal:  Curr Opin Cell Biol       Date:  2020-05-27       Impact factor: 8.382

Review 9.  Shaping Gene Expression by Landscaping Chromatin Architecture: Lessons from a Master.

Authors:  Vittorio Sartorelli; Pier Lorenzo Puri
Journal:  Mol Cell       Date:  2018-06-07       Impact factor: 17.970

Review 10.  Molecular mechanisms driving transcriptional stress responses.

Authors:  Anniina Vihervaara; Fabiana M Duarte; John T Lis
Journal:  Nat Rev Genet       Date:  2018-06       Impact factor: 53.242

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