Ontology highlight
ABSTRACT:
PROVIDER: PRJNA933081 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23379486_1.fastq.gz | Fastqsanger.gz | |||
| SRR23379486_2.fastq.gz | Fastqsanger.gz | |||
| SRR23379487_1.fastq.gz | Fastqsanger.gz | |||
| SRR23379487_2.fastq.gz | Fastqsanger.gz | |||
| SRR23379488_1.fastq.gz | Fastqsanger.gz |
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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: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.
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Project description:Investigation of whole genome gene expression level changes in three S. cerevisiae Y55 mutants, compared to the wild-type strain. The UV-induced mutations enable the mutant strains to ferment high-gravity maltose faster than the WT. The mutants analyzed in this study are further described in Baerends, R.J.S., J.L. Qiu, L. Gautier, and A. Brandt. A high-throughput system for screening of fast-fermenting Saccharomyces cerevisiae strains. Manuscript in preparation.
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Project description:Expression analysis of Saccharomyces cerevisiae TAF5 and taf5 temperature conditional mutants grown at permissive and non-permissive temperature. Investigation of whole genome gene expression level changes in Saccharomyces cerevisae taf5-17, taf5-45, taf5-408 and taf5-10.4 mutants, compared to the wild-type strain. The mutations engineered into the strains confer temperature conditional growth. The mutants analyzed in this study are further described in Layer et. al., 2010. Direct Transactivator-Transcription Factor IID (TFIID) Contacts Drive Yeast Ribosomal Protein Gene Transcription. Journal of Biological Chemistry.
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Project description:Saccharomyces cerevisiae suppressor mutant sequencing
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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.
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Project description:RNA sequencing of Saccharomyces cerevisiae wild type and alanyl-tRNA synthetase mutants grown at 30 degrees and challenged at 37 degrees
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Project description:Centromeric localization of CENP-A (Cse4 in S. cerevisiae, CID in flies, CENP-A in humans) is essential for faithful chromosome segregation. Overexpression of CENP-A leads to its mislocalization and contributes to aneuploidy in yeast, flies, humans and is proposed to promote tumorigenesis in human cancers. Hence, defining molecular mechanisms that promote or prevent mislocalization of CENP-A is an area of active investigation. In budding yeast, evolutionarily conserved histone chaperones Scm3 and chromatin assembly factor-1 (CAF-1) promote localization of Cse4 to centromeric and non-centromeric regions, respectively. Ubiquitin ligases such as Psh1 and Slx5 and histone chaperones (HIR complex) regulate proteolysis of overexpressed Cse4 and prevent its mislocalization to non-centromeric regions. In this study, we have identified sumoylation sites lysine (K) 215/216 in the C-terminus of Cse4 and shown that sumoylation of Cse4 K215/216 facilitates its genome-wide deposition into chromatin when overexpressed. Our results showed reduced levels of sumoylation of mutant Cse4 K215/216R/A (K changed to arginine (R) or alanine (A)) and reduced interaction of mutant Cse4 K215/215R/A with Scm3 and CAF-1 when compared to wild type Cse4. Consistent with these results, levels of Cse4 K215/216R/A in the chromatin fraction at centromeric and non-centromeric regions were reduced. Furthermore, in contrast to GAL-CSE4 which exhibits Synthetic Dosage Lethality (SDL) in psh1Æ, slx5Æ, and hir2Æ strains, GAL-cse4 K215/216R does not exhibit SDL in these strains. Taken together, our results identify and define a role for C-terminal sumoylation of Cse4 for its incorporation into chromatin.
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Project description:Expression analysis of Saccharomyces cerevisiae TAF5 and taf5 temperature conditional mutants grown at permissive and non-permissive temperature. Investigation of whole genome gene expression level changes in Saccharomyces cerevisae taf5-17, taf5-45, taf5-408 and taf5-10.4 mutants, compared to the wild-type strain. The mutations engineered into the strains confer temperature conditional growth. The mutants analyzed in this study are further described in Layer et. al., 2010. Direct Transactivator-Transcription Factor IID (TFIID) Contacts Drive Yeast Ribosomal Protein Gene Transcription. Journal of Biological Chemistry. A twenty chip study using total RNA recovered from four separate wild-type cultures of Saccharomyces cerevisiae and four separate cultures for each of four taf5 temperature conditional mutants (16 mutant cultures). Each chip measures the expression level of 5,777 genes from Saccharomyces S288C with eight 60-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.
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