Literature DB >> 34303933

Phase separation in transcription factor dynamics and chromatin organization.

Kaustubh Wagh1, David A Garcia1, Arpita Upadhyaya2.   

Abstract

Studies over the past decade have highlighted the key role of liquid-liquid phase separation in cellular organization and function. Dynamic compartmentalization of transcription factors and coactivators by such phase-separated condensates regulates the assembly of transcriptional machinery at genomic loci. Although rapid advances in microscopy have demonstrated the ubiquity of such condensates, a rigorous characterization of the physics of phase separation in transcription remains to be carried out. In this review, we discuss theoretical and experimental evidence for biomolecular condensates as dynamic regulators of transcription. Looking beyond, we highlight functional consequences for transcription factor dynamics and gene expression and discuss potential pitfalls of misclassifying biomolecular condensates as liquid droplets in the absence of a rigorous physical description.
Copyright © 2021 Elsevier Ltd. All rights reserved.

Entities:  

Keywords:  Biomolecular condensates; Chromatin organization; Genome organization; Phase separation; Super-enhancer; Transcription factors

Mesh:

Substances:

Year:  2021        PMID: 34303933      PMCID: PMC8794578          DOI: 10.1016/j.sbi.2021.06.009

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  64 in total

1.  Phase separation drives heterochromatin domain formation.

Authors:  Amy R Strom; Alexander V Emelyanov; Mustafa Mir; Dmitry V Fyodorov; Xavier Darzacq; Gary H Karpen
Journal:  Nature       Date:  2017-06-21       Impact factor: 49.962

2.  CTCF and cohesin regulate chromatin loop stability with distinct dynamics.

Authors:  Anders S Hansen; Iryna Pustova; Claudia Cattoglio; Robert Tjian; Xavier Darzacq
Journal:  Elife       Date:  2017-05-03       Impact factor: 8.140

Review 3.  Passive Noise Filtering by Cellular Compartmentalization.

Authors:  Thomas Stoeger; Nico Battich; Lucas Pelkmans
Journal:  Cell       Date:  2016-03-10       Impact factor: 41.582

4.  Pi-Pi contacts are an overlooked protein feature relevant to phase separation.

Authors:  Robert McCoy Vernon; Paul Andrew Chong; Brian Tsang; Tae Hun Kim; Alaji Bah; Patrick Farber; Hong Lin; Julie Deborah Forman-Kay
Journal:  Elife       Date:  2018-02-09       Impact factor: 8.140

5.  MINFLUX nanoscopy delivers 3D multicolor nanometer resolution in cells.

Authors:  Klaus C Gwosch; Jasmin K Pape; Francisco Balzarotti; Philipp Hoess; Jan Ellenberg; Jonas Ries; Stefan W Hell
Journal:  Nat Methods       Date:  2020-01-13       Impact factor: 28.547

6.  RNA polymerase II clustering through carboxy-terminal domain phase separation.

Authors:  Marc Boehning; Claire Dugast-Darzacq; Marija Rankovic; Anders S Hansen; Taekyung Yu; Herve Marie-Nelly; David T McSwiggen; Goran Kokic; Gina M Dailey; Patrick Cramer; Xavier Darzacq; Markus Zweckstetter
Journal:  Nat Struct Mol Biol       Date:  2018-08-20       Impact factor: 15.369

Review 7.  Mechanical Regulation of Transcription: Recent Advances.

Authors:  Kaustubh Wagh; Momoko Ishikawa; David A Garcia; Diana A Stavreva; Arpita Upadhyaya; Gordon L Hager
Journal:  Trends Cell Biol       Date:  2021-03-09       Impact factor: 20.808

8.  HP1 proteins compact DNA into mechanically and positionally stable phase separated domains.

Authors:  Madeline M Keenen; David Brown; Lucy D Brennan; Roman Renger; Harrison Khoo; Christopher R Carlson; Bo Huang; Stephan W Grill; Geeta J Narlikar; Sy Redding
Journal:  Elife       Date:  2021-03-04       Impact factor: 8.140

9.  Pol II phosphorylation regulates a switch between transcriptional and splicing condensates.

Authors:  Yang Eric Guo; John C Manteiga; Jonathan E Henninger; Benjamin R Sabari; Alessandra Dall'Agnese; Nancy M Hannett; Jan-Hendrik Spille; Lena K Afeyan; Alicia V Zamudio; Krishna Shrinivas; Brian J Abraham; Ann Boija; Tim-Michael Decker; Jenna K Rimel; Charli B Fant; Tong Ihn Lee; Ibrahim I Cisse; Phillip A Sharp; Dylan J Taatjes; Richard A Young
Journal:  Nature       Date:  2019-08-07       Impact factor: 49.962

10.  Bridging-induced phase separation induced by cohesin SMC protein complexes.

Authors:  Je-Kyung Ryu; Céline Bouchoux; Hon Wing Liu; Eugene Kim; Masashi Minamino; Ralph de Groot; Allard J Katan; Andrea Bonato; Davide Marenduzzo; Davide Michieletto; Frank Uhlmann; Cees Dekker
Journal:  Sci Adv       Date:  2021-02-10       Impact factor: 14.136

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  4 in total

1.  Protein Condensation in the Nuclear Receptor Family; Implications for Transcriptional Output.

Authors:  Monique D Appelman; Elle E Hollaar; Jurian Schuijers; Saskia W C van Mil
Journal:  Adv Exp Med Biol       Date:  2022       Impact factor: 3.650

2.  JMJD3 intrinsically disordered region links the 3D-genome structure to TGFβ-dependent transcription activation.

Authors:  Marta Vicioso-Mantis; Raquel Fueyo; Claudia Navarro; Sara Cruz-Molina; Wilfred F J van Ijcken; Elena Rebollo; Álvaro Rada-Iglesias; Marian A Martínez-Balbás
Journal:  Nat Commun       Date:  2022-06-07       Impact factor: 17.694

Review 3.  Transcription Regulators and Membraneless Organelles Challenges to Investigate Them.

Authors:  Katarzyna Sołtys; Andrzej Ożyhar
Journal:  Int J Mol Sci       Date:  2021-11-25       Impact factor: 5.923

4.  An integrative multi-omics analysis based on liquid-liquid phase separation delineates distinct subtypes of lower-grade glioma and identifies a prognostic signature.

Authors:  Jianglin Zheng; Zhipeng Wu; Yue Qiu; Xuan Wang; Xiaobing Jiang
Journal:  J Transl Med       Date:  2022-01-29       Impact factor: 5.531

  4 in total

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