Literature DB >> 32497955

The self-stirred genome: large-scale chromatin dynamics, its biophysical origins and implications.

Alexandra Zidovska1.   

Abstract

The organization and dynamics of human genome govern all cellular processes - directly impacting the central dogma of biology - yet are poorly understood, especially at large length scales. Chromatin, the functional form of DNA in cells, undergoes frequent local remodeling and rearrangements to accommodate processes such as transcription, replication and DNA repair. How these local activities contribute to nucleus-wide coherent chromatin motion, where micron-scale regions of chromatin move together over several seconds, remains unclear. Activity of nuclear enzymes was found to drive the coherent chromatin dynamics, however, its biological nature and physical mechanism remain to be revealed. The coherent dynamics leads to a perpetual stirring of the genome, leading to collective gene dynamics over microns and seconds, thus likely contributing to local and global gene-expression patterns. Hence, a possible biological role of chromatin coherence may involve gene regulation.
Copyright © 2020 Elsevier Ltd. All rights reserved.

Entities:  

Year:  2020        PMID: 32497955      PMCID: PMC8164847          DOI: 10.1016/j.gde.2020.03.008

Source DB:  PubMed          Journal:  Curr Opin Genet Dev        ISSN: 0959-437X            Impact factor:   5.578


  75 in total

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2.  Magnetic manipulation of nanorods in the nucleus of living cells.

Authors:  Alfredo Celedon; Christopher M Hale; Denis Wirtz
Journal:  Biophys J       Date:  2011-10-19       Impact factor: 4.033

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

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Journal:  Nature       Date:  1970-08-08       Impact factor: 49.962

5.  Surface Fluctuations and Coalescence of Nucleolar Droplets in the Human Cell Nucleus.

Authors:  Christina M Caragine; Shannon C Haley; Alexandra Zidovska
Journal:  Phys Rev Lett       Date:  2018-10-05       Impact factor: 9.161

6.  Chromatin domains and the interchromatin compartment form structurally defined and functionally interacting nuclear networks.

Authors:  Heiner Albiez; Marion Cremer; Cinzia Tiberi; Lorella Vecchio; Lothar Schermelleh; Sandra Dittrich; Katrin Küpper; Boris Joffe; Tobias Thormeyer; Johann von Hase; Siwei Yang; Karl Rohr; Heinrich Leonhardt; Irina Solovei; Christoph Cremer; Stanislav Fakan; Thomas Cremer
Journal:  Chromosome Res       Date:  2006-11-22       Impact factor: 4.620

7.  Anomalous diffusion, spatial coherence, and viscoelasticity from the energy landscape of human chromosomes.

Authors:  Michele Di Pierro; Davit A Potoyan; Peter G Wolynes; José N Onuchic
Journal:  Proc Natl Acad Sci U S A       Date:  2018-07-09       Impact factor: 11.205

8.  Single nucleosome imaging reveals loose genome chromatin networks via active RNA polymerase II.

Authors:  Ryosuke Nagashima; Kayo Hibino; S S Ashwin; Michael Babokhov; Shin Fujishiro; Ryosuke Imai; Tadasu Nozaki; Sachiko Tamura; Tomomi Tani; Hiroshi Kimura; Michael Shribak; Masato T Kanemaki; Masaki Sasai; Kazuhiro Maeshima
Journal:  J Cell Biol       Date:  2019-03-01       Impact factor: 10.539

Review 9.  The biology and polymer physics underlying large-scale chromosome organization.

Authors:  Shelley Sazer; Helmut Schiessel
Journal:  Traffic       Date:  2017-12-03       Impact factor: 6.215

10.  Super-Resolution Imaging of Higher-Order Chromatin Structures at Different Epigenomic States in Single Mammalian Cells.

Authors:  Jianquan Xu; Hongqiang Ma; Jingyi Jin; Shikhar Uttam; Rao Fu; Yi Huang; Yang Liu
Journal:  Cell Rep       Date:  2018-07-24       Impact factor: 9.423

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  6 in total

1.  Interphase Chromatin Undergoes a Local Sol-Gel Transition upon Cell Differentiation.

Authors:  Iraj Eshghi; Jonah A Eaton; Alexandra Zidovska
Journal:  Phys Rev Lett       Date:  2021-06-04       Impact factor: 9.185

Review 2.  The rich inner life of the cell nucleus: dynamic organization, active flows, and emergent rheology.

Authors:  Alexandra Zidovska
Journal:  Biophys Rev       Date:  2020-10-16

3.  Spatial organization of chromosomes leads to heterogeneous chromatin motion and drives the liquid- or gel-like dynamical behavior of chromatin.

Authors:  Hossein Salari; Marco Di Stefano; Daniel Jost
Journal:  Genome Res       Date:  2021-12-28       Impact factor: 9.438

Review 4.  A Liquid State Perspective on Dynamics of Chromatin Compartments.

Authors:  Rabia Laghmach; Michele Di Pierro; Davit Potoyan
Journal:  Front Mol Biosci       Date:  2022-01-13

5.  Multiscale modeling of genome organization with maximum entropy optimization.

Authors:  Xingcheng Lin; Yifeng Qi; Andrew P Latham; Bin Zhang
Journal:  J Chem Phys       Date:  2021-07-07       Impact factor: 3.488

6.  Liquid-liquid phase separation driven compartmentalization of reactive nucleoplasm.

Authors:  Rabia Laghmach; Davit A Potoyan
Journal:  Phys Biol       Date:  2021-01-07       Impact factor: 2.583

  6 in total

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