Literature DB >> 23751185

Chromatin and DNA replication.

David M MacAlpine1, Geneviève Almouzni.   

Abstract

The size of a eukaryotic genome presents a unique challenge to the cell: package and organize the DNA to fit within the confines of the nucleus while at the same time ensuring sufficient dynamics to allow access to specific sequences and features such as genes and regulatory elements. This is achieved via the dynamic nucleoprotein organization of eukaryotic DNA into chromatin. The basic unit of chromatin, the nucleosome, comprises a core particle with 147 bp of DNA wrapped 1.7 times around an octamer of histones. The nucleosome is a highly versatile and modular structure, both in its composition, with the existence of various histone variants, and through the addition of a series of posttranslational modifications on the histones. This versatility allows for both short-term regulatory responses to external signaling, as well as the long-term and multigenerational definition of large functional chromosomal domains within the nucleus, such as the centromere. Chromatin organization and its dynamics participate in essentially all DNA-templated processes, including transcription, replication, recombination, and repair. Here we will focus mainly on nucleosomal organization and describe the pathways and mechanisms that contribute to assembly of this organization and the role of chromatin in regulating the DNA replication program.

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Year:  2013        PMID: 23751185      PMCID: PMC3721285          DOI: 10.1101/cshperspect.a010207

Source DB:  PubMed          Journal:  Cold Spring Harb Perspect Biol        ISSN: 1943-0264            Impact factor:   10.005


  192 in total

1.  Dual role of DNA intrinsic curvature and flexibility in determining nucleosome stability.

Authors:  C Anselmi; G Bocchinfuso; P De Santis; M Savino; A Scipioni
Journal:  J Mol Biol       Date:  1999-03-12       Impact factor: 5.469

2.  Genome-wide studies highlight indirect links between human replication origins and gene regulation.

Authors:  Jean-Charles Cadoret; Françoise Meisch; Vahideh Hassan-Zadeh; Isabelle Luyten; Claire Guillet; Laurent Duret; Hadi Quesneville; Marie-Noëlle Prioleau
Journal:  Proc Natl Acad Sci U S A       Date:  2008-10-06       Impact factor: 11.205

3.  DNA replication timing of the human beta-globin domain is controlled by histone modification at the origin.

Authors:  Alon Goren; Amalia Tabib; Merav Hecht; Howard Cedar
Journal:  Genes Dev       Date:  2008-04-28       Impact factor: 11.361

4.  Replication-dependent marking of DNA by PCNA facilitates CAF-1-coupled inheritance of chromatin.

Authors:  K Shibahara; B Stillman
Journal:  Cell       Date:  1999-02-19       Impact factor: 41.582

5.  A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning.

Authors:  Anton Valouev; Jeffrey Ichikawa; Thaisan Tonthat; Jeremy Stuart; Swati Ranade; Heather Peckham; Kathy Zeng; Joel A Malek; Gina Costa; Kevin McKernan; Arend Sidow; Andrew Fire; Steven M Johnson
Journal:  Genome Res       Date:  2008-05-13       Impact factor: 9.043

6.  Nucleosome organization in the Drosophila genome.

Authors:  Travis N Mavrich; Cizhong Jiang; Ilya P Ioshikhes; Xiaoyong Li; Bryan J Venters; Sara J Zanton; Lynn P Tomsho; Ji Qi; Robert L Glaser; Stephan C Schuster; David S Gilmour; Istvan Albert; B Franklin Pugh
Journal:  Nature       Date:  2008-04-13       Impact factor: 49.962

Review 7.  Metabolism and regulation of canonical histone mRNAs: life without a poly(A) tail.

Authors:  William F Marzluff; Eric J Wagner; Robert J Duronio
Journal:  Nat Rev Genet       Date:  2008-11       Impact factor: 53.242

8.  A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome.

Authors:  Travis N Mavrich; Ilya P Ioshikhes; Bryan J Venters; Cizhong Jiang; Lynn P Tomsho; Ji Qi; Stephan C Schuster; Istvan Albert; B Franklin Pugh
Journal:  Genome Res       Date:  2008-06-12       Impact factor: 9.043

9.  The histone chaperone Asf1 is dispensable for direct de novo histone deposition in Xenopus egg extracts.

Authors:  Dominique Ray-Gallet; Jean-Pierre Quivy; Herman W W Silljé; Erich A Nigg; Geneviève Almouzni
Journal:  Chromosoma       Date:  2007-06-19       Impact factor: 2.919

10.  Global reorganization of replication domains during embryonic stem cell differentiation.

Authors:  Ichiro Hiratani; Tyrone Ryba; Mari Itoh; Tomoki Yokochi; Michaela Schwaiger; Chia-Wei Chang; Yung Lyou; Tim M Townes; Dirk Schübeler; David M Gilbert
Journal:  PLoS Biol       Date:  2008-10-07       Impact factor: 8.029

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  82 in total

Review 1.  Activation and regulation of H2B-Ubiquitin-dependent histone methyltransferases.

Authors:  Evan J Worden; Cynthia Wolberger
Journal:  Curr Opin Struct Biol       Date:  2019-06-21       Impact factor: 6.809

2.  Construction of Comprehensive Dosage-Matching Core Histone Mutant Libraries for Saccharomyces cerevisiae.

Authors:  Shuangying Jiang; Yan Liu; Ann Wang; Yiran Qin; Maoguo Luo; Qingyu Wu; Jef D Boeke; Junbiao Dai
Journal:  Genetics       Date:  2017-10-30       Impact factor: 4.562

3.  Condensins and 3D Organization of the Interphase Nucleus.

Authors:  Heather A Wallace; Giovanni Bosco
Journal:  Curr Genet Med Rep       Date:  2013-12-01

Review 4.  When proteins play tag: the dynamic nature of the replisome.

Authors:  Stefan H Mueller; Lisanne M Spenkelink; Antoine M van Oijen
Journal:  Biophys Rev       Date:  2019-07-04

5.  SIR2 suppresses replication gaps and genome instability by balancing replication between repetitive and unique sequences.

Authors:  Eric J Foss; Uyen Lao; Emily Dalrymple; Robin L Adrianse; Taylor Loe; Antonio Bedalov
Journal:  Proc Natl Acad Sci U S A       Date:  2017-01-03       Impact factor: 11.205

Review 6.  Expanding the roles of chromatin insulators in nuclear architecture, chromatin organization and genome function.

Authors:  Todd Schoborg; Mariano Labrador
Journal:  Cell Mol Life Sci       Date:  2014-07-11       Impact factor: 9.261

7.  Plant chromatin warms up in Madrid: meeting summary of the 3rd European Workshop on Plant Chromatin 2013, Madrid, Spain.

Authors:  José A Jarillo; Valérie Gaudin; Lars Hennig; Claudia Köhler; Manuel Piñeiro
Journal:  Epigenetics       Date:  2014-02-06       Impact factor: 4.528

8.  DNA repair factor APLF acts as a H2A-H2B histone chaperone through binding its DNA interaction surface.

Authors:  Ivan Corbeski; Klemen Dolinar; Hans Wienk; Rolf Boelens; Hugo van Ingen
Journal:  Nucleic Acids Res       Date:  2018-08-21       Impact factor: 16.971

9.  Delivering nonidentical twins.

Authors:  Thomas A Kunkel; Peter M Burgers
Journal:  Nat Struct Mol Biol       Date:  2014-07-06       Impact factor: 15.369

Review 10.  Regulating DNA replication in bacteria.

Authors:  Kirsten Skarstad; Tsutomu Katayama
Journal:  Cold Spring Harb Perspect Biol       Date:  2013-04-01       Impact factor: 10.005

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