Literature DB >> 22520729

Replication timing and its emergence from stochastic processes.

John Bechhoefer1, Nicholas Rhind.   

Abstract

The temporal organization of DNA replication has puzzled cell biologists since before the mechanism of replication was understood. The realization that replication timing correlates with important features, such as transcription, chromatin structure and genome evolution, and is misregulated in cancer and aging has only deepened the fascination. Many ideas about replication timing have been proposed, but most have been short on mechanistic detail. However, recent work has begun to elucidate basic principles of replication timing. In particular, mathematical modeling of replication kinetics in several systems has shown that the reproducible replication timing patterns seen in population studies can be explained by stochastic origin firing at the single-cell level. This work suggests that replication timing need not be controlled by a hierarchical mechanism that imposes replication timing from a central regulator, but instead results from simple rules that affect individual origins.
Copyright © 2012 Elsevier Ltd. All rights reserved.

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Year:  2012        PMID: 22520729      PMCID: PMC3401328          DOI: 10.1016/j.tig.2012.03.011

Source DB:  PubMed          Journal:  Trends Genet        ISSN: 0168-9525            Impact factor:   11.639


  96 in total

Review 1.  Eukaryotic chromosome DNA replication: where, when, and how?

Authors:  Hisao Masai; Seiji Matsumoto; Zhiying You; Naoko Yoshizawa-Sugata; Masako Oda
Journal:  Annu Rev Biochem       Date:  2010       Impact factor: 23.643

Review 2.  How do Cdc7 and cyclin-dependent kinases trigger the initiation of chromosome replication in eukaryotic cells?

Authors:  Karim Labib
Journal:  Genes Dev       Date:  2010-06-15       Impact factor: 11.361

3.  S-phase progression in mammalian cells: modelling the influence of nuclear organization.

Authors:  Alex Shaw; Pedro Olivares-Chauvet; Apolinar Maya-Mendoza; Dean A Jackson
Journal:  Chromosome Res       Date:  2010-01       Impact factor: 5.239

4.  Replication fork density increases during DNA synthesis in X. laevis egg extracts.

Authors:  J Herrick; P Stanislawski; O Hyrien; A Bensimon
Journal:  J Mol Biol       Date:  2000-07-28       Impact factor: 5.469

Review 5.  How dormant origins promote complete genome replication.

Authors:  J Julian Blow; Xin Quan Ge; Dean A Jackson
Journal:  Trends Biochem Sci       Date:  2011-06-07       Impact factor: 13.807

6.  Genome-wide estimation of firing efficiencies of origins of DNA replication from time-course copy number variation data.

Authors:  Huaien Luo; Juntao Li; Majid Eshaghi; Jianhua Liu; R Krishna Murthy Karuturi
Journal:  BMC Bioinformatics       Date:  2010-05-13       Impact factor: 3.169

7.  Dynamics of DNA replication in yeast.

Authors:  Renata Retkute; Conrad A Nieduszynski; Alessandro de Moura
Journal:  Phys Rev Lett       Date:  2011-08-04       Impact factor: 9.161

8.  The regulation of DNA synthesis and mitosis in multinucleate frog eggs.

Authors:  C F Graham
Journal:  J Cell Sci       Date:  1966-09       Impact factor: 5.285

9.  Do replication forks control late origin firing in Saccharomyces cerevisiae?

Authors:  Emilie Ma; Olivier Hyrien; Arach Goldar
Journal:  Nucleic Acids Res       Date:  2011-11-15       Impact factor: 16.971

10.  Replicon clusters are stable units of chromosome structure: evidence that nuclear organization contributes to the efficient activation and propagation of S phase in human cells.

Authors:  D A Jackson; A Pombo
Journal:  J Cell Biol       Date:  1998-03-23       Impact factor: 10.539

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  45 in total

1.  Replication origins run (ultra) deep.

Authors:  David M Gilbert
Journal:  Nat Struct Mol Biol       Date:  2012-08       Impact factor: 15.369

Review 2.  Cell cycle control in the early embryonic development of aquatic animal species.

Authors:  Joseph C Siefert; Emily A Clowdus; Christopher L Sansam
Journal:  Comp Biochem Physiol C Toxicol Pharmacol       Date:  2015-10-17       Impact factor: 3.228

3.  Selectivity of ORC binding sites and the relation to replication timing, fragile sites, and deletions in cancers.

Authors:  Benoit Miotto; Zhe Ji; Kevin Struhl
Journal:  Proc Natl Acad Sci U S A       Date:  2016-07-19       Impact factor: 11.205

Review 4.  Positive and Negative Regulation of DNA Replication Initiation.

Authors:  Qiliang Ding; Amnon Koren
Journal:  Trends Genet       Date:  2020-07-29       Impact factor: 11.639

5.  High-resolution profiling of Drosophila replication start sites reveals a DNA shape and chromatin signature of metazoan origins.

Authors:  Federico Comoglio; Tommy Schlumpf; Virginia Schmid; Remo Rohs; Christian Beisel; Renato Paro
Journal:  Cell Rep       Date:  2015-04-23       Impact factor: 9.423

Review 6.  How and why multiple MCMs are loaded at origins of DNA replication.

Authors:  Shankar P Das; Nicholas Rhind
Journal:  Bioessays       Date:  2016-05-13       Impact factor: 4.345

7.  Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations.

Authors:  Christopher Maffeo; Han-Yi Chou; Aleksei Aksimentiev
Journal:  Adv Theory Simul       Date:  2019-02-12

8.  Cell-to-cell variability and robustness in S-phase duration from genome replication kinetics.

Authors:  Qing Zhang; Federico Bassetti; Marco Gherardi; Marco Cosentino Lagomarsino
Journal:  Nucleic Acids Res       Date:  2017-08-21       Impact factor: 16.971

Review 9.  Replicating Large Genomes: Divide and Conquer.

Authors:  Juan Carlos Rivera-Mulia; David M Gilbert
Journal:  Mol Cell       Date:  2016-06-02       Impact factor: 17.970

Review 10.  Replication timing and transcriptional control: beyond cause and effect-part III.

Authors:  Juan Carlos Rivera-Mulia; David M Gilbert
Journal:  Curr Opin Cell Biol       Date:  2016-04-23       Impact factor: 8.382

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