Saccharomyces cerevisiae
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ABSTRACT:
PROVIDER: PRJNA384989 | ENA |
REPOSITORIES: ENA
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Project description:Analysis of gene expression by RNA Seq in mutants of Psh1, Cac2, or the double mutant relative to WT upon overexpression of Cse4 in Saccharomyces cerevisiae.
| PRJNA384990 | ENA
Project description:Correct localization of the centromeric histone variant CenH3/CENP-A/Cse4 is an important part of faithful chromosome segregation. Mislocalization of CenH3 could lead to ectopic centromere formation and missegregation, and could affect DNA replication and transcription. CENP-A is often overexpressed and mislocalized in cancer genomes, but the underlying mechanisms are not understood. One major regulator of Cse4 deposition is Psh1, an E3 ubiquitin ligase that controls levels of Cse4 to prevent deposition into noncentromeric regions. We present evidence that Chromatin assembly factor-1 (CAF-1), an evolutionarily conserved histone H3/H4 chaperone shown previously to interact with CenH3 in flies and human cells, regulates Cse4 deposition in budding yeast. Yeast CAF-1 (yCAF-1) is a heterotrimeric protein complex consisting of CAC1, CAC2, and CAC3, which interacts with Cse4, and can assemble Cse4 nucleosomes in vitro. yCAF-1 regulates the stability of both soluble and chromatin associated Cse4. Loss of yCAF-1 can rescue growth defects and changes in gene expression associated with Cse4 deposition that occur in the absence of Psh1-mediated proteolysis. Incorporation of Cse4 into promoter nucleosomes at transcriptionally active genes depends on yCAF-1. Overall our findings suggest CAF-1 can act as a CenH3 chaperone, regulating levels and incorporation of CenH3 in chromatin. Furthermore, the misincorporation of CenH3 at promoter regions may have negative consequences for gene expression.
2017-09-01 | GSE98396 | GEO
Project description:Correct localization of the centromeric histone variant CenH3/CENP-A/Cse4 is an important part of faithful chromosome segregation. Mislocalization of CenH3 could lead to ectopic centromere formation and missegregation, and could affect DNA replication and transcription. CENP-A is often overexpressed and mislocalized in cancer genomes, but the underlying mechanisms are not understood. One major regulator of Cse4 deposition is Psh1, an E3 ubiquitin ligase that controls levels of Cse4 to prevent deposition into noncentromeric regions. We present evidence that Chromatin assembly factor-1 (CAF-1), an evolutionarily conserved histone H3/H4 chaperone shown previously to interact with CenH3 in flies and human cells, regulates Cse4 deposition in budding yeast. Yeast CAF-1 (yCAF-1) is a heterotrimeric protein complex consisting of CAC1, CAC2, and CAC3, which interacts with Cse4, and can assemble Cse4 nucleosomes in vitro. yCAF-1 regulates the stability of both soluble and chromatin associated Cse4. Loss of yCAF-1 can rescue growth defects and changes in gene expression associated with Cse4 deposition that occur in the absence of Psh1-mediated proteolysis. Incorporation of Cse4 into promoter nucleosomes at transcriptionally active genes depends on yCAF-1. Overall our findings suggest CAF-1 can act as a CenH3 chaperone, regulating levels and incorporation of CenH3 in chromatin. Furthermore, the misincorporation of CenH3 at promoter regions may have negative consequences for gene expression.
2017-09-01 | GSE98395 | 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. 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: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
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: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.
2020-02-21 | GSE145602 | GEO
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. A single-dye 12-plex array chip study using double-stranded DNA prepared from messenger RNA purified from total RNA recovered from three separate Saccharomyces cerevisiae Y55 wild-type cultures and 3x three separate cultures each corresponding to a fast-fermenting UV-induced mutant (mutant 1, 2 and 3), during fermentation of high-gravity maltose at day 2. Each array on the 12-plex chip measures the expression level of 5,777 genes from Saccharomyces cerevisiae S288C with eight 60-mer probes per gene, with three-fold technical redundancy.
2013-10-25 | E-GEOD-25015 | biostudies-arrayexpress
Project description:Saccharomyces cerevisiae were treated with 1280 drugs from the Prestwick chemical library. Intracellular polar metabolite extracts were collected and measured in negative mode by flow injection analysis. In addition, intracellular metabolite extracts were collected and measured for inducible overexpression mutants in yeast membrane proteins.
2020-11-13 | MSV000086451 | MassIVE
Project description:Saccharomyces cerevisiae inducible overexpression mutants were treated with the indicated concentration of inducers for 1.5 and 3 hours before the intracellular metabolome was collected. Samples were subjected to LCMS analysis in negative mode with separation by an InfinityLab Poroshell 120 HILIC-Z column (2.1 x 100 mm, 2.7 um, Agilent)
2021-05-13 | MSV000087421 | MassIVE