Unknown,Transcriptomics,Genomics,Proteomics

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Strain abundance assay of barcoded heterozygous and homozygous yeast single gene deletion strains exposed to 87 psychoactive drugs

ABSTRACT: To profile off-target effects of psychoactive drugs, 87 genome-wide drug fitness assays (of which 5 were performed in duplicate) and 18 genome-wide control experiments were performed in Saccharomyces cerevisiae. Heterozygous and homozygous yeast single gene deletion strains from the BY collection of the Saccharomyces cerevisiae genome deletion consortium were used.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Elke Ericson

PROVIDER: E-MTAB-34 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Annotating Low Abundance and Transient RNAs in Yeast using Tiling Microarrays and Ultra High-throughput Sequencing Reveals New Transcripts that are not Conserved Across Closely Related Yeast Species A complete description of the transcriptome of an organism is crucial for a comprehensive understanding of how it functions, how its transcriptional networks are controlled, and may provide insights into the organism’s evolution. Despite the status of Saccharomyces cerevisiae as arguably the most well studied model eukaryote, we still do not have a full catalog or understanding of all its genes. In order to interrogate the transcriptome of S. cerevisiae for low abundance or rapidly turned over transcripts, we deleted elements of the RNA degradation machinery with the goal of preferentially increasing the relative abundance of such transcripts. We then used high-resolution tiling microarrays and ultra high-throughput sequencing (UHTS) to identify, map and validate unannotated transcripts that are more abundant in the RNA degradation mutants relative to wild-type cells. We identified 365 currently unannotated transcripts, the majority presumably representing low abundance or short-lived RNAs, of which 185 are previously unknown and unique to this study. It is likely that many of these are cryptic unstable transcripts (CUTs), which are rapidly degraded and whose function(s) within the cell are still unclear, while others may be novel functional transcripts. Of the 185 transcripts we identified as novel to our study, greater than 80 percent come from regions of the genome that have lower conservation scores amongst closely related yeast species than 85 percent of the verified ORFs in S. cerevisiae. Such regions of the genome have typically been less well studied, and by definition transcripts from these regions will distinguish S. cerevisiae from these closely related species. Keywords: Saccharomyces cerevisiae, transcriptome, RNA-Seq, RNA degradation, XRN1, RRP6, LSM1, PAT1, Salt Shock, NaCl

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Strain abundance assay of barcoded heterozygous and homozygous yeast single gene deletion strains exposed to 87 psychoactive drugs

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