Phys Rev Lett. 2005 Jun 24;94(24):248103. Epub 2005 Jun 23.

From DNA sequence analysis to modeling replication in the human genome.

Brodie Of Brodie EB, Nicolay S, Touchon M, Audit B, d'Aubenton-Carafa Y, Thermes C, Arneodo A.

Source

Laboratoire Joliot-Curie (CNRS), Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France.

Abstract

We explore the large-scale behavior of nucleotide compositional strand asymmetries along human chromosomes. As we observe for 7 of 9 origins of replication experimentally identified so far, the (TA+GC) skew displays rather sharp upward jumps, with a linear decreasing profile in between two successive jumps. We present a model of replication with well positioned replication origins and random terminations that accounts for the observed characteristic serrated skew profiles. We succeed in identifying 287 pairs of putative adjacent replication origins with an origin spacing approximately 1-2 Mbp that are likely to correspond to replication foci observed in interphase nuclei and recognized as stable structures that persist throughout subsequent cell generations.

PMID:: 16090582; [PubMed - indexed for MEDLINE]

Publication Types, MeSH Terms

Publication Types

Research Support, Non-U.S. Gov't

MeSH Terms

LinkOut - more resources

Full Text Sources

Supplemental Content

Save items

Related citations in PubMed

Replication-associated strand asymmetries in mammalian genomes: toward detection of replication origins. [Proc Natl Acad Sci U S A. 2005]
Replication-associated strand asymmetries in mammalian genomes: toward detection of replication origins.
Touchon M, Nicolay S, Audit B, Brodie of Brodie EB, d'Aubenton-Carafa Y, Arneodo A, Thermes C. Proc Natl Acad Sci U S A. 2005 Jul 12; 102(28):9836-41. Epub 2005 Jun 28.
DNA replication timing data corroborate in silico human replication origin predictions. [Phys Rev Lett. 2007]
DNA replication timing data corroborate in silico human replication origin predictions.
Audit B, Nicolay S, Huvet M, Touchon M, d'Aubenton-Carafa Y, Thermes C, Arneodo A. Phys Rev Lett. 2007 Dec 14; 99(24):248102. Epub 2007 Dec 12.
Replication-associated mutational asymmetry in the human genome. [Mol Biol Evol. 2011]
Replication-associated mutational asymmetry in the human genome.
Chen CL, Duquenne L, Audit B, Guilbaud G, Rappailles A, Baker A, Huvet M, d'Aubenton-Carafa Y, Hyrien O, Arneodo A, et al. Mol Biol Evol. 2011 Aug; 28(8):2327-37. Epub 2011 Mar 2.
Review From GC skews to wavelets: a gentle guide to the analysis of compositional asymmetries in genomic data. [Biochimie. 2008]
Review From GC skews to wavelets: a gentle guide to the analysis of compositional asymmetries in genomic data.
Touchon M, Rocha EP. Biochimie. 2008 Apr; 90(4):648-59. Epub 2007 Sep 29.
Review Heterogeneity of eukaryotic replicons, replicon clusters, and replication foci. [Chromosoma. 2000]
Review Heterogeneity of eukaryotic replicons, replicon clusters, and replication foci.
Berezney R, Dubey DD, Huberman JA. Chromosoma. 2000 Mar; 108(8):471-84.

See reviews... See all...

Cited by 7 PubMed Central articles

Replication fork polarity gradients revealed by megabase-sized U-shaped replication timing domains in human cell lines. [PLoS Comput Biol. 2012]
Replication fork polarity gradients revealed by megabase-sized U-shaped replication timing domains in human cell lines.
Baker A, Audit B, Chen CL, Moindrot B, Leleu A, Guilbaud G, Rappailles A, Vaillant C, Goldar A, Mongelard F, et al. PLoS Comput Biol. 2012 Apr; 8(4):e1002443. Epub 2012 Apr 5.
5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells. [Genome Biol. 2011]
5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells.
Stroud H, Feng S, Morey Kinney S, Pradhan S, Jacobsen SE. Genome Biol. 2011 Jun 20; 12(6):R54. Epub 2011 Jun 20.
Open chromatin encoded in DNA sequence is the signature of 'master' replication origins in human cells. [Nucleic Acids Res. 2009]
Open chromatin encoded in DNA sequence is the signature of 'master' replication origins in human cells.
Audit B, Zaghloul L, Vaillant C, Chevereau G, d'Aubenton-Carafa Y, Thermes C, Arneodo A. Nucleic Acids Res. 2009 Oct; 37(18):6064-75. Epub 2009 Aug 10.

See all...

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

From DNA sequence analysis to modeling replication in the human genome.
From DNA sequence analysis to modeling replication in the human genome.
Phys Rev Lett. 2005 Jun 24 ;94(24):248103. Epub 2005 Jun 23 .

PubMed
High incidence of tardive dyskinesia in older outpatients on low doses of neurol...
High incidence of tardive dyskinesia in older outpatients on low doses of neuroleptics.
Psychopharmacol Bull. 1992 ;28(1):87-92.

PubMed
Experimental observation of the 1/3 magnetization plateau in the diamond-chain c...
Experimental observation of the 1/3 magnetization plateau in the diamond-chain compound Cu3(CO3)2(OH)2.
Phys Rev Lett. 2005 Jun 10 ;94(22):227201. Epub 2005 Jun 6 .

PubMed
Buprenorphine for cocaine and opiate dependence.
Buprenorphine for cocaine and opiate dependence.
Psychopharmacol Bull. 1992 ;28(1):15-9.

PubMed
Reflex modification in psychosis-prone young adults.
Reflex modification in psychosis-prone young adults.
Psychophysiology. 1992 Jan ;29(1):8-16.

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Result Filters

Display Settings:

Send to: