Literature DB >> 25956973

Principles of chromatin organization in yeast: relevance of polymer models to describe nuclear organization and dynamics.

Renjie Wang1, Julien Mozziconacci2, Aurélien Bancaud3, Olivier Gadal4.   

Abstract

Nuclear organization can impact on all aspects of the genome life cycle. This organization is thoroughly investigated by advanced imaging and chromosome conformation capture techniques, providing considerable amount of datasets describing the spatial organization of chromosomes. In this review, we will focus on polymer models to describe chromosome statics and dynamics in the yeast Saccharomyces cerevisiae. We suggest that the equilibrium configuration of a polymer chain tethered at both ends and placed in a confined volume is consistent with the current literature, implying that local chromatin interactions play a secondary role in yeast nuclear organization. Future challenges are to reach an integrated multi-scale description of yeast chromosome organization, which is crucially needed to improve our understanding of the regulation of genomic transaction.
Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

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Year:  2015        PMID: 25956973     DOI: 10.1016/j.ceb.2015.04.004

Source DB:  PubMed          Journal:  Curr Opin Cell Biol        ISSN: 0955-0674            Impact factor:   8.382


  17 in total

1.  Physical Modeling of Dynamic Coupling between Chromosomal Loci.

Authors:  Thomas J Lampo; Andrew S Kennard; Andrew J Spakowitz
Journal:  Biophys J       Date:  2016-01-19       Impact factor: 4.033

2.  Rouse model with transient intramolecular contacts on a timescale of seconds recapitulates folding and fluctuation of yeast chromosomes.

Authors:  Marius Socol; Renjie Wang; Daniel Jost; Pascal Carrivain; Cédric Vaillant; Eric Le Cam; Vincent Dahirel; Christophe Normand; Kerstin Bystricky; Jean-Marc Victor; Olivier Gadal; Aurélien Bancaud
Journal:  Nucleic Acids Res       Date:  2019-07-09       Impact factor: 16.971

Review 3.  Formation of Chromatin Subcompartments by Phase Separation.

Authors:  Fabian Erdel; Karsten Rippe
Journal:  Biophys J       Date:  2018-04-06       Impact factor: 4.033

4.  Condensin Depletion Causes Genome Decompaction Without Altering the Level of Global Gene Expression in Saccharomyces cerevisiae.

Authors:  Matthew Robert Paul; Tovah Elise Markowitz; Andreas Hochwagen; Sevinç Ercan
Journal:  Genetics       Date:  2018-07-03       Impact factor: 4.562

5.  The vacuole shapes the nucleus and the ribosomal DNA loop during mitotic delays.

Authors:  Emiliano Matos-Perdomo; Silvia Santana-Sosa; Jessel Ayra-Plasencia; Sara Medina-Suárez; Félix Machín
Journal:  Life Sci Alliance       Date:  2022-08-12

6.  Exogenous artificial DNA forms chromatin structure with active transcription in yeast.

Authors:  Jianting Zhou; Chao Zhang; Ran Wei; Mingzhe Han; Songduo Wang; Kaiguang Yang; Lihua Zhang; Weigang Chen; Mingzhang Wen; Cheng Li; Wei Tao; Ying-Jin Yuan
Journal:  Sci China Life Sci       Date:  2021-12-27       Impact factor: 10.372

7.  Entropy gives rise to topologically associating domains.

Authors:  Paula A Vasquez; Caitlin Hult; David Adalsteinsson; Josh Lawrimore; Mark G Forest; Kerry Bloom
Journal:  Nucleic Acids Res       Date:  2016-06-02       Impact factor: 16.971

Review 8.  Polymer perspective of genome mobilization.

Authors:  Colleen J Lawrimore; Josh Lawrimore; Yunyan He; Sergio Chavez; Kerry Bloom
Journal:  Mutat Res       Date:  2020-05-26       Impact factor: 2.433

9.  Enrichment of dynamic chromosomal crosslinks drive phase separation of the nucleolus.

Authors:  Caitlin Hult; David Adalsteinsson; Paula A Vasquez; Josh Lawrimore; Maggie Bennett; Alyssa York; Diana Cook; Elaine Yeh; Mark Gregory Forest; Kerry Bloom
Journal:  Nucleic Acids Res       Date:  2017-11-02       Impact factor: 16.971

10.  Mechanistic Modeling of Dose and Dose Rate Dependences of Radiation-Induced DNA Double Strand Break Rejoining Kinetics in Saccharomyces cerevisiae.

Authors:  Igor Shuryak
Journal:  PLoS One       Date:  2016-01-07       Impact factor: 3.240

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