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Genome-wide replication landscape of Candida glabrata.

Descorps-Declère S, Saguez C, Cournac A, Marbouty M, Rolland T, Ma L, Bouchier C, Moszer I, Dujon B, Koszul R, Richard GF - BMC Biol. (2015)

Bottom Line: Using chromosome conformation capture, we also show that early origins tend to cluster whereas non-subtelomeric megasatellites do not cluster in the yeast nucleus.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.

View Article: PubMed Central - PubMed

Affiliation: Institut Pasteur, Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), F-75015, Paris, France. stephane.descorps-declere@pasteur.fr.

ABSTRACT

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.

No MeSH data available.


Related in: MedlinePlus

ARS capture and fitnesses. a Distribution of distances between ARSs and replication origins. The observed distribution is shown in blue. The simulation of 1,000 independent experiments is shown in gray (see text). The dotted red line corresponds to the 3-kb distance limit that was chosen to define bona fide origins. b Coverage of each ARS at G50 (y axis) as compared to G0 (x axis). The dotted red line corresponds to a coverage ratio 1/1. ARSs with the highest G50 coverage are labeled. c Same as b, but for G100 coverage of each ARS (y axis), as compared to G50 coverage (x axis). ARS autonomously replicating sequence
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Fig5: ARS capture and fitnesses. a Distribution of distances between ARSs and replication origins. The observed distribution is shown in blue. The simulation of 1,000 independent experiments is shown in gray (see text). The dotted red line corresponds to the 3-kb distance limit that was chosen to define bona fide origins. b Coverage of each ARS at G50 (y axis) as compared to G0 (x axis). The dotted red line corresponds to a coverage ratio 1/1. ARSs with the highest G50 coverage are labeled. c Same as b, but for G100 coverage of each ARS (y axis), as compared to G50 coverage (x axis). ARS autonomously replicating sequence

Mentions: ARSs were numbered on each chromosome, according to their position, from the left to the right telomere. ARS positions were compared to replication origins, and the distance between each ARS and the closest replication origin was computed. About half of ARSs (150/275, 55 %) were found within 10 kb of a replication origin (Fig. 5a, blue bars ), with a majority of those within 3 kb (83/150). The set of origins close to these 83 ARSs were considered as bona fide origins and were used for subsequent statistical analyses. As a control, 1,000 random sets of 275 DNA fragments (random ARSs) were generated genome wide. The same number of random ARSs as compared to real ARSs was generated per chromosome, and their distance to the closest origin was calculated. The average result of these 1,000 simulations followed a normal distribution (mean = 18.5 kb, sigma = 3.3 kb) and was strikingly different from the observed distribution (Fig. 5a, gray bars).Fig. 5


Genome-wide replication landscape of Candida glabrata.

Descorps-Declère S, Saguez C, Cournac A, Marbouty M, Rolland T, Ma L, Bouchier C, Moszer I, Dujon B, Koszul R, Richard GF - BMC Biol. (2015)

ARS capture and fitnesses. a Distribution of distances between ARSs and replication origins. The observed distribution is shown in blue. The simulation of 1,000 independent experiments is shown in gray (see text). The dotted red line corresponds to the 3-kb distance limit that was chosen to define bona fide origins. b Coverage of each ARS at G50 (y axis) as compared to G0 (x axis). The dotted red line corresponds to a coverage ratio 1/1. ARSs with the highest G50 coverage are labeled. c Same as b, but for G100 coverage of each ARS (y axis), as compared to G50 coverage (x axis). ARS autonomously replicating sequence
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4556013&req=5

Fig5: ARS capture and fitnesses. a Distribution of distances between ARSs and replication origins. The observed distribution is shown in blue. The simulation of 1,000 independent experiments is shown in gray (see text). The dotted red line corresponds to the 3-kb distance limit that was chosen to define bona fide origins. b Coverage of each ARS at G50 (y axis) as compared to G0 (x axis). The dotted red line corresponds to a coverage ratio 1/1. ARSs with the highest G50 coverage are labeled. c Same as b, but for G100 coverage of each ARS (y axis), as compared to G50 coverage (x axis). ARS autonomously replicating sequence
Mentions: ARSs were numbered on each chromosome, according to their position, from the left to the right telomere. ARS positions were compared to replication origins, and the distance between each ARS and the closest replication origin was computed. About half of ARSs (150/275, 55 %) were found within 10 kb of a replication origin (Fig. 5a, blue bars ), with a majority of those within 3 kb (83/150). The set of origins close to these 83 ARSs were considered as bona fide origins and were used for subsequent statistical analyses. As a control, 1,000 random sets of 275 DNA fragments (random ARSs) were generated genome wide. The same number of random ARSs as compared to real ARSs was generated per chromosome, and their distance to the closest origin was calculated. The average result of these 1,000 simulations followed a normal distribution (mean = 18.5 kb, sigma = 3.3 kb) and was strikingly different from the observed distribution (Fig. 5a, gray bars).Fig. 5

Bottom Line: Using chromosome conformation capture, we also show that early origins tend to cluster whereas non-subtelomeric megasatellites do not cluster in the yeast nucleus.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.

View Article: PubMed Central - PubMed

Affiliation: Institut Pasteur, Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), F-75015, Paris, France. stephane.descorps-declere@pasteur.fr.

ABSTRACT

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.

No MeSH data available.


Related in: MedlinePlus