Asymmetry Indices for Analysis and Prediction of Replication Origins in Eukaryotic Genomes.
| Title: | Asymmetry Indices for Analysis and Prediction of Replication Origins in Eukaryotic Genomes. |
|---|---|
| Authors: | Marsolier-Kergoat, Marie-Claude1 mcmk@cea.fr, Nieduszynski, Conrad A.2 |
| Source: | PLoS ONE. Sep2012, Vol. 7 Issue 9, Special section p1-11. 11p. |
| Subject Terms: | *DNA replication, *SACCHAROMYCES cerevisiae, *KLUYVEROMYCES marxianus, *YEAST research, *EUKARYOTES, *GENOMICS |
| Abstract: | DNA replication was recently shown to induce the formation of compositional skews in the genomes of the yeasts Saccharomyces cerevisiae and Kluyveromyces lactis. In this work, I have characterized further GC and TA skew variations in the vicinity of S. cerevisiae replication origins and termination sites, and defined asymmetry indices for origin analysis and prediction. The presence of skew jumps at some termination sites in the S. cerevisiae genome was established. The majority of S. cerevisiae replication origins are marked by an oriented consensus sequence called ACS, but no evidence could be found for asymmetric origin firing that would be linked to ACS orientation. Asymmetry indices related to GC and TA skews were defined, and a global asymmetry index IGC,TA was described. IGC,TA was found to strongly correlate with origin efficiency in S. cerevisiae and to allow the determination of sets of intergenes significantly enriched in origin loci. The generalized use of asymmetry indices for origin prediction in naive genomes implies the determination of the direction of the skews, i.e. the identification of which strand, leading or lagging, is enriched in G and which one is enriched in T. Recent work indicates that in Candida albicans and in several related species, centromeres contain early and efficient replication origins. It has been proposed that the skew jumps observed at these positions would reflect the activity of these origins, thus allowing to determine the direction of the skews in these genomes. However, I show here that the skew jumps at C. albicans centromeres are not related to replication and that replication-associated GC and TA skews in C. albicans have in fact the opposite directions of what was proposed. [ABSTRACT FROM AUTHOR] |
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| Items | – Name: Title Label: Title Group: Ti Data: Asymmetry Indices for Analysis and Prediction of Replication Origins in Eukaryotic Genomes. – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AR" term="%22Marsolier-Kergoat%2C+Marie-Claude%22">Marsolier-Kergoat, Marie-Claude</searchLink><relatesTo>1</relatesTo><i> mcmk@cea.fr</i><br /><searchLink fieldCode="AR" term="%22Nieduszynski%2C+Conrad+A%2E%22">Nieduszynski, Conrad A.</searchLink><relatesTo>2</relatesTo> – Name: TitleSource Label: Source Group: Src Data: <searchLink fieldCode="JN" term="%22PLoS+ONE%22">PLoS ONE</searchLink>. Sep2012, Vol. 7 Issue 9, Special section p1-11. 11p. – Name: Subject Label: Subject Terms Group: Su Data: *<searchLink fieldCode="DE" term="%22DNA+replication%22">DNA replication</searchLink><br />*<searchLink fieldCode="DE" term="%22SACCHAROMYCES+cerevisiae%22">SACCHAROMYCES cerevisiae</searchLink><br />*<searchLink fieldCode="DE" term="%22KLUYVEROMYCES+marxianus%22">KLUYVEROMYCES marxianus</searchLink><br />*<searchLink fieldCode="DE" term="%22YEAST+research%22">YEAST research</searchLink><br />*<searchLink fieldCode="DE" term="%22EUKARYOTES%22">EUKARYOTES</searchLink><br />*<searchLink fieldCode="DE" term="%22GENOMICS%22">GENOMICS</searchLink> – Name: Abstract Label: Abstract Group: Ab Data: DNA replication was recently shown to induce the formation of compositional skews in the genomes of the yeasts Saccharomyces cerevisiae and Kluyveromyces lactis. In this work, I have characterized further GC and TA skew variations in the vicinity of S. cerevisiae replication origins and termination sites, and defined asymmetry indices for origin analysis and prediction. The presence of skew jumps at some termination sites in the S. cerevisiae genome was established. The majority of S. cerevisiae replication origins are marked by an oriented consensus sequence called ACS, but no evidence could be found for asymmetric origin firing that would be linked to ACS orientation. Asymmetry indices related to GC and TA skews were defined, and a global asymmetry index IGC,TA was described. IGC,TA was found to strongly correlate with origin efficiency in S. cerevisiae and to allow the determination of sets of intergenes significantly enriched in origin loci. The generalized use of asymmetry indices for origin prediction in naive genomes implies the determination of the direction of the skews, i.e. the identification of which strand, leading or lagging, is enriched in G and which one is enriched in T. Recent work indicates that in Candida albicans and in several related species, centromeres contain early and efficient replication origins. It has been proposed that the skew jumps observed at these positions would reflect the activity of these origins, thus allowing to determine the direction of the skews in these genomes. However, I show here that the skew jumps at C. albicans centromeres are not related to replication and that replication-associated GC and TA skews in C. albicans have in fact the opposite directions of what was proposed. [ABSTRACT FROM AUTHOR] – Name: AbstractSuppliedCopyright Label: Group: Ab Data: <i>Copyright of PLoS ONE is the property of Public Library of Science and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.) |
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| RecordInfo | BibRecord: BibEntity: Identifiers: – Type: doi Value: 10.1371/journal.pone.0045050 Languages: – Code: eng Text: English PhysicalDescription: Pagination: PageCount: 11 StartPage: 1 Subjects: – SubjectFull: DNA replication Type: general – SubjectFull: SACCHAROMYCES cerevisiae Type: general – SubjectFull: KLUYVEROMYCES marxianus Type: general – SubjectFull: YEAST research Type: general – SubjectFull: EUKARYOTES Type: general – SubjectFull: GENOMICS Type: general Titles: – TitleFull: Asymmetry Indices for Analysis and Prediction of Replication Origins in Eukaryotic Genomes. Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Marsolier-Kergoat, Marie-Claude – PersonEntity: Name: NameFull: Nieduszynski, Conrad A. IsPartOfRelationships: – BibEntity: Dates: – D: 01 M: 09 Text: Sep2012 Type: published Y: 2012 Identifiers: – Type: issn-print Value: 19326203 Numbering: – Type: volume Value: 7 – Type: issue Value: 9 Titles: – TitleFull: PLoS ONE Type: main |
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