Literature DB >> 33771451

Phase separation in genome organization across evolution.

Marina Feric1, Tom Misteli2.   

Abstract

Phase separation is emerging as a paradigm to explain the self-assembly and organization of membraneless bodies in the cell. Recent advances show that this principle also extends to nucleoprotein complexes, including DNA-based structures. We discuss here recent observations on the role of phase separation in genome organization across the evolutionary spectrum from bacteria to mammals. These findings suggest that molecular interactions amongst DNA-binding proteins evolved to form a variety of biomolecular condensates with distinct material properties that affect genome organization and function. We suggest that phase separation contributes to genome organization across evolution and that the resulting phase behavior of genomes may underlie regulatory mechanisms and disease. Published by Elsevier Ltd.

Entities:  

Keywords:  biomolecular condensates; evolution; genome organization; phase separation; transcription

Mesh:

Year:  2021        PMID: 33771451      PMCID: PMC8286288          DOI: 10.1016/j.tcb.2021.03.001

Source DB:  PubMed          Journal:  Trends Cell Biol        ISSN: 0962-8924            Impact factor:   21.167


  117 in total

1.  A Liquid-to-Solid Phase Transition of the ALS Protein FUS Accelerated by Disease Mutation.

Authors:  Avinash Patel; Hyun O Lee; Louise Jawerth; Shovamayee Maharana; Marcus Jahnel; Marco Y Hein; Stoyno Stoynov; Julia Mahamid; Shambaditya Saha; Titus M Franzmann; Andrej Pozniakovski; Ina Poser; Nicola Maghelli; Loic A Royer; Martin Weigert; Eugene W Myers; Stephan Grill; David Drechsel; Anthony A Hyman; Simon Alberti
Journal:  Cell       Date:  2015-08-27       Impact factor: 41.582

2.  Design and self-assembly of two-dimensional DNA crystals.

Authors:  E Winfree; F Liu; L A Wenzler; N C Seeman
Journal:  Nature       Date:  1998-08-06       Impact factor: 49.962

3.  Dynamic Organization of Chromatin Domains Revealed by Super-Resolution Live-Cell Imaging.

Authors:  Tadasu Nozaki; Ryosuke Imai; Mai Tanbo; Ryosuke Nagashima; Sachiko Tamura; Tomomi Tani; Yasumasa Joti; Masaru Tomita; Kayo Hibino; Masato T Kanemaki; Kerstin S Wendt; Yasushi Okada; Takeharu Nagai; Kazuhiro Maeshima
Journal:  Mol Cell       Date:  2017-07-14       Impact factor: 17.970

4.  Live-cell superresolution microscopy reveals the organization of RNA polymerase in the bacterial nucleoid.

Authors:  Mathew Stracy; Christian Lesterlin; Federico Garza de Leon; Stephan Uphoff; Pawel Zawadzki; Achillefs N Kapanidis
Journal:  Proc Natl Acad Sci U S A       Date:  2015-07-29       Impact factor: 11.205

5.  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

6.  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

7.  Phase separation of 53BP1 determines liquid-like behavior of DNA repair compartments.

Authors:  Sinan Kilic; Aleksandra Lezaja; Marco Gatti; Eliana Bianco; Jone Michelena; Ralph Imhof; Matthias Altmeyer
Journal:  EMBO J       Date:  2019-07-01       Impact factor: 11.598

Review 8.  Evidence for and against Liquid-Liquid Phase Separation in the Nucleus.

Authors:  Peng A; Stephanie C Weber
Journal:  Noncoding RNA       Date:  2019-11-01

9.  Ki-67 acts as a biological surfactant to disperse mitotic chromosomes.

Authors:  Sara Cuylen; Claudia Blaukopf; Antonio Z Politi; Thomas Müller-Reichert; Beate Neumann; Ina Poser; Jan Ellenberg; Anthony A Hyman; Daniel W Gerlich
Journal:  Nature       Date:  2016-06-29       Impact factor: 49.962

10.  Nucleoid remodeling during environmental adaptation is regulated by HU-dependent DNA bundling.

Authors:  Soumya G Remesh; Subhash C Verma; Jian-Hua Chen; Axel A Ekman; Carolyn A Larabell; Sankar Adhya; Michal Hammel
Journal:  Nat Commun       Date:  2020-06-09       Impact factor: 17.694

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  20 in total

1.  ASCL1 phosphorylation and ID2 upregulation are roadblocks to glioblastoma stem cell differentiation.

Authors:  Roberta Azzarelli; Aoibheann McNally; Claudia Dell'Amico; Marco Onorati; Benjamin Simons; Anna Philpott
Journal:  Sci Rep       Date:  2022-02-11       Impact factor: 4.379

2.  Droplets take DNA by force.

Authors:  Marina Feric
Journal:  Nat Phys       Date:  2021-07-08       Impact factor: 20.034

3.  Mesoscale structure-function relationships in mitochondrial transcriptional condensates.

Authors:  Marina Feric; Azadeh Sarfallah; Furqan Dar; Dmitry Temiakov; Rohit V Pappu; Tom Misteli
Journal:  Proc Natl Acad Sci U S A       Date:  2022-10-03       Impact factor: 12.779

Review 4.  The mechanobiology of nuclear phase separation.

Authors:  Daniel S W Lee; Amy R Strom; Clifford P Brangwynne
Journal:  APL Bioeng       Date:  2022-04-28

5.  Drosophila insulator proteins exhibit in vivo liquid-liquid phase separation properties.

Authors:  Bright Amankwaa; Todd Schoborg; Mariano Labrador
Journal:  Life Sci Alliance       Date:  2022-07-19

6.  Deneddylation of PML/RARα reconstructs functional PML nuclear bodies via orchestrating phase separation to eradicate APL.

Authors:  Xuejing Shao; Yingqian Chen; Aixiao Xu; Danyan Xiang; Wei Wang; Wenxin Du; Yunpeng Huang; Xingya Zhang; Minyi Cai; Zhimei Xia; Yi Wang; Ji Cao; Yan Zhang; Bo Yang; Qiaojun He; Meidan Ying
Journal:  Cell Death Differ       Date:  2022-02-22       Impact factor: 12.067

Review 7.  Interphase epichromatin: last refuge for the 30-nm chromatin fiber?

Authors:  Peng Xu; Julia Mahamid; Marco Dombrowski; Wolfgang Baumeister; Ada L Olins; Donald E Olins
Journal:  Chromosoma       Date:  2021-06-05       Impact factor: 4.316

Review 8.  Merging Established Mechanisms with New Insights: Condensates, Hubs, and the Regulation of RNA Polymerase II Transcription.

Authors:  Megan Palacio; Dylan J Taatjes
Journal:  J Mol Biol       Date:  2021-08-30       Impact factor: 5.469

Review 9.  Deciphering the Complexity of 3D Chromatin Organization Driving Lymphopoiesis and Lymphoid Malignancies.

Authors:  Laurianne Scourzic; Eralda Salataj; Effie Apostolou
Journal:  Front Immunol       Date:  2021-05-14       Impact factor: 7.561

Review 10.  Nuclear Protein Condensates and Their Properties in Regulation of Gene Expression.

Authors:  Wei Li; Hao Jiang
Journal:  J Mol Biol       Date:  2021-07-14       Impact factor: 6.151

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