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Genome-wide replication landscape of Candida glabrata

BACKGROUND: The opportunistic pathogen Candida glabrata is a member of the Saccharomycetaceae yeasts. Like its close relative Saccharomyces cerevisiae, it underwent a whole-genome duplication followed by an extensive loss of genes. Its genome contains a large number of very long tandem repeats, call...

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Autores principales: Descorps-Declère, Stéphane, Saguez, Cyril, Cournac, Axel, Marbouty, Martial, Rolland, Thomas, Ma, Laurence, Bouchier, Christiane, Moszer, Ivan, Dujon, Bernard, Koszul, Romain, Richard, Guy-Franck
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4556013/
https://www.ncbi.nlm.nih.gov/pubmed/26329162
http://dx.doi.org/10.1186/s12915-015-0177-6
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author Descorps-Declère, Stéphane
Saguez, Cyril
Cournac, Axel
Marbouty, Martial
Rolland, Thomas
Ma, Laurence
Bouchier, Christiane
Moszer, Ivan
Dujon, Bernard
Koszul, Romain
Richard, Guy-Franck
author_facet Descorps-Declère, Stéphane
Saguez, Cyril
Cournac, Axel
Marbouty, Martial
Rolland, Thomas
Ma, Laurence
Bouchier, Christiane
Moszer, Ivan
Dujon, Bernard
Koszul, Romain
Richard, Guy-Franck
author_sort Descorps-Declère, Stéphane
collection PubMed
description BACKGROUND: The opportunistic pathogen Candida glabrata is a member of the Saccharomycetaceae yeasts. Like its close relative Saccharomyces cerevisiae, it underwent a whole-genome duplication followed by an extensive loss of genes. Its genome contains a large number of very long tandem repeats, called megasatellites. In order to determine the whole replication program of the C. glabrata genome and its general chromosomal organization, we used deep-sequencing and chromosome conformation capture experiments. RESULTS: We identified 253 replication fork origins, genome wide. Centromeres, HML and HMR loci, and most histone genes are replicated early, whereas natural chromosomal breakpoints are located in late-replicating regions. In addition, 275 autonomously replicating sequences (ARS) were identified during ARS-capture experiments, and their relative fitness was determined during growth competition. Analysis of ARSs allowed us to identify a 17-bp consensus, similar to the S. cerevisiae ARS consensus sequence but slightly more constrained. Megasatellites are not in close proximity to replication origins or termini. Using chromosome conformation capture, we also show that early origins tend to cluster whereas non-subtelomeric megasatellites do not cluster in the yeast nucleus. CONCLUSIONS: Despite a shorter cell cycle, the C. glabrata replication program shares unexpected striking similarities to S. cerevisiae, in spite of their large evolutionary distance and the presence of highly repetitive large tandem repeats in C. glabrata. No correlation could be found between the replication program and megasatellites, suggesting that their formation and propagation might not be directly caused by replication fork initiation or termination. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12915-015-0177-6) contains supplementary material, which is available to authorized users.
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spelling pubmed-45560132015-09-02 Genome-wide replication landscape of Candida glabrata Descorps-Declère, Stéphane Saguez, Cyril Cournac, Axel Marbouty, Martial Rolland, Thomas Ma, Laurence Bouchier, Christiane Moszer, Ivan Dujon, Bernard Koszul, Romain Richard, Guy-Franck BMC Biol Research Article BACKGROUND: The opportunistic pathogen Candida glabrata is a member of the Saccharomycetaceae yeasts. Like its close relative Saccharomyces cerevisiae, it underwent a whole-genome duplication followed by an extensive loss of genes. Its genome contains a large number of very long tandem repeats, called megasatellites. In order to determine the whole replication program of the C. glabrata genome and its general chromosomal organization, we used deep-sequencing and chromosome conformation capture experiments. RESULTS: We identified 253 replication fork origins, genome wide. Centromeres, HML and HMR loci, and most histone genes are replicated early, whereas natural chromosomal breakpoints are located in late-replicating regions. In addition, 275 autonomously replicating sequences (ARS) were identified during ARS-capture experiments, and their relative fitness was determined during growth competition. Analysis of ARSs allowed us to identify a 17-bp consensus, similar to the S. cerevisiae ARS consensus sequence but slightly more constrained. Megasatellites are not in close proximity to replication origins or termini. Using chromosome conformation capture, we also show that early origins tend to cluster whereas non-subtelomeric megasatellites do not cluster in the yeast nucleus. CONCLUSIONS: Despite a shorter cell cycle, the C. glabrata replication program shares unexpected striking similarities to S. cerevisiae, in spite of their large evolutionary distance and the presence of highly repetitive large tandem repeats in C. glabrata. No correlation could be found between the replication program and megasatellites, suggesting that their formation and propagation might not be directly caused by replication fork initiation or termination. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12915-015-0177-6) contains supplementary material, which is available to authorized users. BioMed Central 2015-09-02 /pmc/articles/PMC4556013/ /pubmed/26329162 http://dx.doi.org/10.1186/s12915-015-0177-6 Text en © Descorps-Declère et al. 2015 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/ (http://creativecommons.org/licenses/by/4.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Descorps-Declère, Stéphane
Saguez, Cyril
Cournac, Axel
Marbouty, Martial
Rolland, Thomas
Ma, Laurence
Bouchier, Christiane
Moszer, Ivan
Dujon, Bernard
Koszul, Romain
Richard, Guy-Franck
Genome-wide replication landscape of Candida glabrata
title Genome-wide replication landscape of Candida glabrata
title_full Genome-wide replication landscape of Candida glabrata
title_fullStr Genome-wide replication landscape of Candida glabrata
title_full_unstemmed Genome-wide replication landscape of Candida glabrata
title_short Genome-wide replication landscape of Candida glabrata
title_sort genome-wide replication landscape of candida glabrata
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4556013/
https://www.ncbi.nlm.nih.gov/pubmed/26329162
http://dx.doi.org/10.1186/s12915-015-0177-6
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