Literature DB >> 18233493

DNA replication timing data corroborate in silico human replication origin predictions.

B Audit1, S Nicolay, M Huvet, M Touchon, Y d'Aubenton-Carafa, C Thermes, A Arneodo.   

Abstract

We develop a wavelet-based multiscale pattern recognition methodology to disentangle the replication- from the transcription-associated compositional strand asymmetries observed in the human genome. Comparing replication skew profiles to recent high-resolution replication timing data reveals that most of the putative replication origins that border the so-identified replication domains are replicated earlier than their surroundings whereas the central regions replicate late in the S phase. We discuss the implications of this first experimental confirmation of these replication origin predictions that are likely to be early replicating and active in most tissues.

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Year:  2007        PMID: 18233493     DOI: 10.1103/PhysRevLett.99.248102

Source DB:  PubMed          Journal:  Phys Rev Lett        ISSN: 0031-9007            Impact factor:   9.161


  17 in total

1.  Gene regulatory network inference using out of equilibrium statistical mechanics.

Authors:  Arndt Benecke
Journal:  HFSP J       Date:  2008-07-23

2.  Chromatin state marks cell-type- and gender-specific replication of the Drosophila genome.

Authors:  Michaela Schwaiger; Michael B Stadler; Oliver Bell; Hubertus Kohler; Edward J Oakeley; Dirk Schübeler
Journal:  Genes Dev       Date:  2009-03-01       Impact factor: 11.361

3.  Multiscale analysis of genome-wide replication timing profiles using a wavelet-based signal-processing algorithm.

Authors:  Benjamin Audit; Antoine Baker; Chun-Long Chen; Aurélien Rappailles; Guillaume Guilbaud; Hanna Julienne; Arach Goldar; Yves d'Aubenton-Carafa; Olivier Hyrien; Claude Thermes; Alain Arneodo
Journal:  Nat Protoc       Date:  2012-12-13       Impact factor: 13.491

4.  Linking the DNA strand asymmetry to the spatio-temporal replication program: II. Accounting for neighbor-dependent substitution rates.

Authors:  A Baker; C L Chen; H Julienne; B Audit; Y d'Aubenton-Carafa; C Thermes; A Arneodo
Journal:  Eur Phys J E Soft Matter       Date:  2012-11-27       Impact factor: 1.890

5.  Linking the DNA strand asymmetry to the spatio-temporal replication program. I. About the role of the replication fork polarity in genome evolution.

Authors:  A Baker; H Julienne; C L Chen; B Audit; Y d'Aubenton-Carafa; C Thermes; A Arneodo
Journal:  Eur Phys J E Soft Matter       Date:  2012-09-26       Impact factor: 1.890

6.  DNA replication and strand asymmetry in prokaryotic and mitochondrial genomes.

Authors:  Xuhua Xia
Journal:  Curr Genomics       Date:  2012-03       Impact factor: 2.236

7.  3D chromatin conformation correlates with replication timing and is conserved in resting cells.

Authors:  Benoit Moindrot; Benjamin Audit; Petra Klous; Antoine Baker; Claude Thermes; Wouter de Laat; Philippe Bouvet; Fabien Mongelard; Alain Arneodo
Journal:  Nucleic Acids Res       Date:  2012-08-08       Impact factor: 16.971

8.  Analysis of fine-scale mammalian evolutionary breakpoints provides new insight into their relation to genome organisation.

Authors:  Claire Lemaitre; Lamia Zaghloul; Marie-France Sagot; Christian Gautier; Alain Arneodo; Eric Tannier; Benjamin Audit
Journal:  BMC Genomics       Date:  2009-07-24       Impact factor: 3.969

9.  Open chromatin encoded in DNA sequence is the signature of 'master' replication origins in human cells.

Authors:  Benjamin Audit; Lamia Zaghloul; Cédric Vaillant; Guillaume Chevereau; Yves d'Aubenton-Carafa; Claude Thermes; Alain Arneodo
Journal:  Nucleic Acids Res       Date:  2009-08-10       Impact factor: 16.971

10.  Human genome replication proceeds through four chromatin states.

Authors:  Hanna Julienne; Azedine Zoufir; Benjamin Audit; Alain Arneodo
Journal:  PLoS Comput Biol       Date:  2013-10-10       Impact factor: 4.475

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