Cryptococcus amylolentus
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ABSTRACT:
PROVIDER: PRJNA376407 | ENA |
REPOSITORIES: ENA
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Project description:Species within the human pathogenic Cryptococcus species complex are major threats to public health, causing about one million infections globally each year. Cryptococcus amylolentus is the most closely known related species of the pathogenic Cryptococcus species complex, and it is non-pathogenic. Additionally, while pathogenic Cryptococcus species have bipolar mating systems with a single large MAT locus that represents a derived state in Basidiomycetes, C. amylolentus has a tetrapolar mating system with two MAT loci (P/R and HD) located on different chromosomes. Thus, studying C. amylolentus will shed light on the origin and evolution of pathogenesis, as well as the transition from tetrapolar to bipolar mating systems in the pathogenic Cryptococcus species. In this study, we sequenced, assembled, and annotated the genomes of two C. amylolentus isolates, CBS6039 and CBS6273, which are sexual and interfertile. Genome comparison between the two C. amylolentus isolates identified the boundaries and the complete gene contents of the P/R and HD MAT loci. Also, bioinformatics and ChIP-seq analyses showed that C. amylolentus has regional centromeres that are enriched with species-specific transposable and repetitive elements, similar to the centromeric structures in the pathogenic Cryptococcus species. Additionally, we found that while neither of the P/R and HD loci in C. amylolentus is physically linked to its centromere, both MAT loci exhibit centromere linkage in meiosis, suggesting the presence of recombinational suppressors and/or epistatic gene interactions in the inter MAT-CEN regions. Furthermore, genomic comparison between C. amylolentus and pathogenic Cryptococcus species provides evidence that chromosomal rearrangements mediated by intercentromeric recombination have occurred after the two lineages split from their common ancestor. We propose a model in which the evolution of the bipolar mating system was initiated by an ectopic recombination event mediated by repetitive elements located within the centromeric regions and shared between chromosomes. This translocation brought the P/R and HD loci onto the same chromosome, and was followed by chromosomal rearrangements that resulted in the two MAT loci becoming physically linked and eventually fused to form the single contiguous MAT locus that is now extant in the pathogenic Cryptococcus species.
2018-04-08 | GSE95128 | GEO
Project description:Sequencing of progeny from crosses between Cryptococcus amylolentus and a putative Tsuchiyaea wingfieldii isolate to examine species boundaries. Genome sequencing
| PRJNA387705 | ENA
Project description:Accurate chromosome segregation requires centromeres (CENs), the chromosomal sites where kinetochores form, to bridge DNA and attach to microtubules. In contrast to most eukaryotes, Saccharomyces cerevisiae possesses sequence-defined point centromeres. Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) of four kinetochore components reveals regions of overlapping, extra-centromeric protein localization upon overproduction of the centromeric histone, Cse4 (CENP-A or CenH3). These identified sequences enhance proper plasmid and chromosome segregation, and are termed Centromere-like Regions (CLRs). CLRs form in close proximity to S. cerevisiae CENs and share characteristics typical of point and regional centromeres. CLR sequences are conserved among related budding yeasts, suggesting a role in vivo. These studies provide new insights into the origin and evolution of centromeres. ChIP-Seq analysis of the kinetochore components Cse4, Mif2, Ndc10 and Ndc80 in budding yeast strains (Saccharomyces cerevisiae) with normal and elevated levels of Cse4
2013-01-18 | E-GEOD-31466 | biostudies-arrayexpress
Project description:Precise localization of the histone H3 variant CENP-A(Cse4) to centromeres is essential for accurate chromosome segregation. In budding yeast, CENP-A(Cse4) is regulated by ubiquitin-mediated proteolysis to ensure its exclusive localization to the centromere. Overexpression of CENP-A(Cse4) is lethal when the CENP-A(Cse4) E3 ubiquitin ligase, Psh1, is deleted. To identify the genomic sites of CENP-A(Cse4) mislocalization in this condition, we investigated the genome-wide mislocalization pattern of CENP-A(Cse4) by ChIP-seq.
2016-03-08 | GSE69695 | GEO
Project description:Genome and transcriptome sequencing of Cryptococcus amylolentus (CBS6039 isolate)
| PRJEB19939 | ENA
Project description:High resolution ChIP-seq mapping, supported by in vitro reconstitution studies, suggests that the Cse4 nucleosome is a hemisome that occupies the ~80-bp AT-rich CDEII sequence. H4S47C-anchored cleavage mapping of S. cerevisiae centromeres
2014-04-15 | E-GEOD-51949 | biostudies-arrayexpress
Project description:The evolutionarily conserved F-box proteins Met30 and Cdc4 interact with Cse4 in vivo and cooperatively regulate cellular levels of Cse4 by ubiquitin-mediated proteolysis. To survey genomewide localization of Cse4 in met30-6 and cdc4-1 mutants, chromatin immunoprecipitation (ChIP) was carried out in strains expressing HA-tagged Cse4 from its endogenous promoter. Prominent Cse4 peaks were observed only at centromeres (CENs) in all three strains, and a statistically significant increase of Cse4 enrichment at CENs was observed in the mutants. Though extracentromeric peaks of Cse4 accumulation are detected in both wild-type and mutant strains, peak enrichment (vs. the 10-kb local background) in these regions is much lower than that observed for any of the 16 centromeres, and there is no statistically significant difference in Cse4 enrichment at non-CEN peaks between wild-type and mutants. This analysis reveals that the increased mislocalization of Cse4 in met30-6 and cdc4-1 strains detected by Cse4 staining on chromosome spreads is not the result of high levels of enrichment at discrete extracentromeric loci; rather, endogenously expressed Cse4 in met30-6 and cdc4-1 strains accumulates at low levels across the genome.
2019-04-03 | GSE129195 | GEO
Project description:Precise localization of the histone H3 variant CENP-A(Cse4) to centromeres is essential for accurate chromosome segregation. In budding yeast, CENP-A(Cse4) is regulated by ubiquitin-mediated proteolysis to ensure its exclusive localization to the centromere. Overexpression of CENP-A(Cse4) is lethal when the CENP-A(Cse4) E3 ubiquitin ligase, Psh1, is deleted. CENP-A(Cse4) mislocalizes to promoters in this condition, so we investigated if there was an effect on gene expression of downstream genes using RNA-seq.
2016-03-08 | GSE77596 | GEO