Project description:This entry contains the proteomic files from a data set of RNAs, proteins, metabolites and lipids analyzed from the same staged samples of S. cerevisiae cells across the cell cycle. Actively growing (un-arrested) diploid cells were collected by elutriation as 8 distinct size pools across the cell cycle in triplicate. Yeast in these 24 aliquots were lysed and soluble and insoluble proteins were prepared for shotgun LC-MS/MS mass spectrometry analysis.
Project description:For the first time in any system, we generated experiment-matched datasets of the levels of RNAs, proteins, metabolites, and lipids from un-arrested, growing, and synchronously dividing yeast cells.
Project description:RNAi, a gene-silencing pathway triggered by double-stranded RNA, is conserved in diverse eukaryotic species but has been lost in the model budding yeast, Saccharomyces cerevisiae. We report that RNAi is present in other budding-yeast species, including Saccharomyces castellii and Candida albicans. These species use noncanonical Dicer proteins to generate siRNAs, which mostly correspond to transposable elements and Y´ subtelomeric repeats. In S. castellii, RNAi mutants are viable but have excess Y´ mRNA levels. In S. cerevisiae, introducing Dicer and Argonaute of S. castellii restores RNAi, and the reconstituted pathway silences endogenous retrotransposons. These results identify a novel class of Dicer proteins, bring the tool of RNAi to the study of budding yeasts, and bring the tools of budding yeast to the study of RNAi.
Project description:RNAi, a gene-silencing pathway triggered by double-stranded RNA, is conserved in diverse eukaryotic species but has been lost in the model budding yeast, Saccharomyces cerevisiae. We report that RNAi is present in other budding-yeast species, including Saccharomyces castellii and Candida albicans. These species use noncanonical Dicer proteins to generate siRNAs, which mostly correspond to transposable elements and YM-BM-4 subtelomeric repeats. In S. castellii, RNAi mutants are viable but have excess YM-BM-4 mRNA levels. In S. cerevisiae, introducing Dicer and Argonaute of S. castellii restores RNAi, and the reconstituted pathway silences endogenous retrotransposons. These results identify a novel class of Dicer proteins, bring the tool of RNAi to the study of budding yeasts, and bring the tools of budding yeast to the study of RNAi. Employ high-throughput sequencing of endogenous small RNAs from the budding yeasts Saccharomyces castellii, Kluyveromyces polysporus, Candida albicans, Saccharomyces cerevisiae, and Saccharomyces bayanus.
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
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.
Project description:Here we studied the budding yeast Lachancea kluyveri, a cousin of the model Saccharomyces cerevisiae, in order to try to understand the mechanism responsible for the absence of meiotic recombination on its almost entire sex chromosome (Brion et al. 2017). We performed meiotic DSB mapping using CC-seq (Gittens 2019). Briefly, we observed a distribution of meiotic DSBs mainly in gene promoters as in S. cerevisiae and a depletion within Lakl0C-left (the 1 Mb long domain on the sex chromosome with no meiotic recombination). Also, we noted a poor conservation of DSB hotspots strength between L. kluyveri and S. cerevisiae.