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Saccharomyces cerevisiae

ABSTRACT: Genes identified by poly(A)+ transcriptome sequencing as overexpressed in trf5-Δ98-117

PROVIDER: PRJNA327115 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR3726660.fastq.gz	Fastqsanger.gz
	SRR3726661.fastq.gz	Fastqsanger.gz
	SRR3726662.fastq.gz	Fastqsanger.gz
	SRR3726663.fastq.gz	Fastqsanger.gz

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Genes identified by poly(A)+ transcriptome sequencing as overexpressed in trf5-Î?98-117

Project description:Purpose: To study the effects of disrupting the Trf5-Mtr4 interaction Methods: Analyzed TRF5 and trf5-Î?98-117 strains by transcriptome sequencing of poly(A)+ RNA Results: The set of most significantly affected genes included 71 that were overexpressed in trf5-Î?98-117 and only 5 that were down-regulated.The set of 71 overexpressed genes was predominated by known TRAMP substrates Conclusions: Disruption of the Trf5-Mtr4 interaction results in a snoRNA processing defect Duplicate RNA samples of trf4Î?, trf5Î? yeast strains expressing either TRF5 or trf5-Î?98-117 were enriched for poly(A)+ transcripts and converted to a sequencing library. Transcriptome sequencing was performed on a HiSeq 2500. Each sequenced library yielded between 10 and 14 million 50nt reads that were mapped to the annotated yeast genes using Bowtie. Significantly up- or down-regulated genes in the trf5-Î?98-117 mutant were identified via edgeR.

2016-06-29 | E-GEOD-83827 | biostudies-arrayexpress

Genes identified by poly(A)+ transcriptome sequencing as overexpressed in trf5-Δ98-117

Project description:Purpose: To study the effects of disrupting the Trf5-Mtr4 interaction Methods: Analyzed TRF5 and trf5-Δ98-117 strains by transcriptome sequencing of poly(A)+ RNA Results: The set of most significantly affected genes included 71 that were overexpressed in trf5-Δ98-117 and only 5 that were down-regulated.The set of 71 overexpressed genes was predominated by known TRAMP substrates Conclusions: Disruption of the Trf5-Mtr4 interaction results in a snoRNA processing defect

2016-06-29 | GSE83827 | GEO

Saccharomyces cerevisiae ARO80 overexpression

Project description:The transcription factor ARO80 was overexpressed using the GEV system and gene expression assayed at T=0,30,90,180 minutes.

2015-06-01 | GSE59864 | GEO

Expression data from Saccharomyces cerevisiae with Rnase H overexpression

Project description:Transcripts up- or down-regulated comparing a strain where Rnase H is ectopically overexpressed versus wild type (empty vector); assessing the effect of DNA:RNA hybrid degradation on the transcriptome.

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Dbf4-Dependent Kinase (DDK)-Mediated Proteolysis of CENP-A Prevents Mislocalization of CENP-A in Saccharomyces cerevisiae

Project description:Restricting the localization of the centromeric histone H3 variant CENP-A to centromeres is essential to prevent chromosomal instability (CIN). Mislocalization of overexpressed CENP-A contributes to CIN in yeast, fly, and human cells. CENP-A is overexpressed in many cancers. Therefore, defining mechanisms that prevent CENP-A mislocalization will help us understand how CENP-A overexpression contributes to CIN in cancer. A genome-wide screen to characterize essential genes required for growth when CENP-A is overexpressed identified the replication initiation Dbf4-Dependent Kinase (DDK) complex. We show that DDK regulates ubiquitin-mediated proteolysis of Cse4 and prevents mislocalization of Cse4 independently of its role in DNA replication.

2020-04-04 | GSE148068 | GEO

Saccharomyces cerevisiae 3' poly(A) site mapping

Project description:The use of alternative polyadenylation sites is common and affects the post-transcriptional fate of mRNA, including its stability, localization, and translation. Here we present a method for genome-wide and strand-specific mapping of poly(A) sites and quantification of RNA levels at unprecedented efficiency by using an on-cluster dark T-fill procedure on the Illumina sequencing platform. Our method outperforms former protocols in quality and throughput, and reveals new insights into polyadenylation in Saccharomyces cerevisiae.

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Project description:Budding yeast mRNA poly(A) site mapping

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Saccharomyces cerevisiae

Project description:Saccharomyces cerevisiae 3' poly(A) site mapping

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Saccharomyces cerevisiae

Project description:Expression profile of ACC-overexpressed wild type yeast strain

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The molecular effects of cordycepin on RNA synthesis in Saccharomyces cerevisiae

Project description:Cordycepin (3’ deoxyadenosine) is a biologically active compound that, when incorporated during RNA synthesis in vitro, provokes chain termination due to the absence of a 3’ hydroxyl moiety. We were interested in the effects mediated by this drug in vivo and analysed its impact on RNA metabolism of yeast. Our results support the view that cordycepin-triphosphate (CoTP) is the toxic component that is limiting cell growth through inhibition of RNA synthesis. Unexpectedly, cordycepin treatment modulated 3’ end heterogeneity of ACT1 and ASC1 mRNAs and rapidly induced extended transcripts derived from CYH2 and NEL025c loci. Moreover, cordycepin ameliorated the growth defects of poly(A) polymerase mutants and the pap1-1 mutation neutralized the effects of the drug on gene expression. Our observations are consistent with an epistatic relationship between poly(A) polymerase function and cordycepin action and suggest that a major mode of cordycepin activity reduces 3’ end formation efficiency independently of its potential to terminate RNA chain elongation. Finally, chemical-genetic profiling revealed genome-wide pathways linked to cordycepin activity and identified novel genes involved in poly(A) homeostasis. Keywords: response to drug treatment

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