Literature DB >> 25447077

Mapping replication origin sequences in eukaryotic chromosomes.

Haiqing Fu1, Emilie Besnard, Romain Desprat, Michael Ryan, Malik Kahli, Jean-Marc Lemaitre, Mirit I Aladjem.   

Abstract

Recent advances in genome-sequencing technology have led to the complete mapping of DNA replication initiation sites in the human genome. This thorough origin mapping facilitates understanding of the relationship between replication initiation events, transcription, and chromatin modifications, and allows the characterization of consensus sequences of potential replication origins. This unit provides a detailed protocol for isolation and sequence analysis of nascent DNA strands. Two variations of the protocol based on non-overlapping assumptions are described below, addressing potential bias issues for whole-genome analyses.
Copyright © 2014 John Wiley & Sons, Inc.

Entities:  

Keywords:  DNA replication; next-generation sequencing (NGS); replication origins

Mesh：

Year:  2014        PMID： 25447077      PMCID： PMC4274620          DOI： 10.1002/0471143030.cb2220s65

Source DB:  PubMed          Journal:  Curr Protoc Cell Biol        ISSN： 1934-2616


  5 in total

1.  Unraveling cell type-specific and reprogrammable human replication origin signatures associated with G-quadruplex consensus motifs.

Authors:  Emilie Besnard; Amélie Babled; Laure Lapasset; Ollivier Milhavet; Hugues Parrinello; Christelle Dantec; Jean-Michel Marin; Jean-Marc Lemaitre
Journal:  Nat Struct Mol Biol       Date:  2012-07-01       Impact factor: 15.369

2.  Genome-wide depletion of replication initiation events in highly transcribed regions.

Authors:  Melvenia M Martin; Michael Ryan; RyangGuk Kim; Anna L Zakas; Haiqing Fu; Chii Mei Lin; William C Reinhold; Sean R Davis; Sven Bilke; Hongfang Liu; James H Doroshow; Mark A Reimers; Manuel S Valenzuela; Yves Pommier; Paul S Meltzer; Mirit I Aladjem
Journal:  Genome Res       Date:  2011-08-03       Impact factor: 9.043

3.  Discrete start sites for DNA synthesis in the yeast ARS1 origin.

Authors:  A K Bielinsky; S A Gerbi
Journal:  Science       Date:  1998-01-02       Impact factor: 47.728

4.  Tissue- and age-specific DNA replication patterns at the CTG/CAG-expanded human myotonic dystrophy type 1 locus.

Authors:  John D Cleary; Stéphanie Tomé; Arturo López Castel; Gagan B Panigrahi; Laurent Foiry; Katharine A Hagerman; Hana Sroka; David Chitayat; Geneviève Gourdon; Christopher E Pearson
Journal:  Nat Struct Mol Biol       Date:  2010-08-15       Impact factor: 15.369

5.  Allele-specific genome-wide profiling in human primary erythroblasts reveal replication program organization.

Authors:  Rituparna Mukhopadhyay; Julien Lajugie; Nicolas Fourel; Ari Selzer; Michael Schizas; Boris Bartholdy; Jessica Mar; Chii Mei Lin; Melvenia M Martin; Michael Ryan; Mirit I Aladjem; Eric E Bouhassira
Journal:  PLoS Genet       Date:  2014-05-01       Impact factor: 5.917
  5 in total
  7 in total

1.  Convergence of SIRT1 and ATR signaling to modulate replication origin dormancy.

Authors:  Bhushan L Thakur; Adrian M Baris; Haiqing Fu; Christophe E Redon; Lorinc S Pongor; Sara Mosavarpour; Jacob M Gross; Sang-Min Jang; Robin Sebastian; Koichi Utani; Lisa M Jenkins; Fred E Indig; Mirit I Aladjem
Journal:  Nucleic Acids Res       Date:  2022-05-20       Impact factor: 19.160

2.  SLFN11 Blocks Stressed Replication Forks Independently of ATR.

Authors:  Junko Murai; Sai-Wen Tang; Elisabetta Leo; Simone A Baechler; Christophe E Redon; Hongliang Zhang; Muthana Al Abo; Vinodh N Rajapakse; Eijiro Nakamura; Lisa M Miller Jenkins; Mirit I Aladjem; Yves Pommier
Journal:  Mol Cell       Date:  2018-02-01       Impact factor: 17.970

3.  Dynamics of replication origin over-activation.

Authors:  Haiqing Fu; Christophe E Redon; Bhushan L Thakur; Koichi Utani; Robin Sebastian; Sang-Min Jang; Jacob M Gross; Sara Mosavarpour; Anna B Marks; Sophie Z Zhuang; Sarah B Lazar; Mishal Rao; Shira T Mencer; Adrian M Baris; Lorinc S Pongor; Mirit I Aladjem
Journal:  Nat Commun       Date:  2021-06-08       Impact factor: 14.919

4.  Distinct epigenetic features of differentiation-regulated replication origins.

Authors:  Owen K Smith; RyanGuk Kim; Haiqing Fu; Melvenia M Martin; Chii Mei Lin; Koichi Utani; Ya Zhang; Anna B Marks; Marc Lalande; Stormy Chamberlain; Maxwell W Libbrecht; Eric E Bouhassira; Michael C Ryan; William S Noble; Mirit I Aladjem
Journal:  Epigenetics Chromatin       Date:  2016-05-10       Impact factor: 4.954

5.  Temporal association of ORCA/LRWD1 to late-firing origins during G1 dictates heterochromatin replication and organization.

Authors:  Yating Wang; Abid Khan; Anna B Marks; Owen K Smith; Sumanprava Giri; Yo-Chuen Lin; Rachel Creager; David M MacAlpine; Kannanganattu V Prasanth; Mirit I Aladjem; Supriya G Prasanth
Journal:  Nucleic Acids Res       Date:  2017-03-17       Impact factor: 16.971

6.  Meiotic recombination mirrors patterns of germline replication in mice and humans.

Authors:  Florencia Pratto; Kevin Brick; Gang Cheng; Kwan-Wood Gabriel Lam; Jeffrey M Cloutier; Daisy Dahiya; Stephen R Wellard; Philip W Jordan; R Daniel Camerini-Otero
Journal:  Cell       Date:  2021-07-13       Impact factor: 66.850

7.  High-resolution Repli-Seq defines the temporal choreography of initiation, elongation and termination of replication in mammalian cells.

Authors:  Peiyao A Zhao; Takayo Sasaki; David M Gilbert
Journal:  Genome Biol       Date:  2020-03-24       Impact factor: 13.583
  7 in total

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