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Genetic and pharmacological evidence for kinetic competition between alternative poly(A) sites in yeast - 4tU cordycepin treatment with rpb1 slow mutant

ABSTRACT: Genetic and pharmacological evidence for kinetic competition between alternative poly(A) sites in yeast - 4tU cordycepin treatment with rpb1 slow mutant

PROVIDER: PRJNA675091 | ENA |

REPOSITORIES: ENA

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Genetic and pharmacological evidence for kinetic competition between alternative poly(A) sites in yeast - 4tU cordycepin treatment with rpb1 slow mutant

Project description:mPAT approach using an anchored oligo-dT (TV12VN) primer to determine changes to 3'UTR length in yeast with a slow RNA polymerase II mutant rpb1-1, complemented with wild-type RPB1 or a slow rpb1 mutant plasmid, upon cordycepin treatment and new transcription using 4-thiouracil (4tU) labelling of RNA. This appears as a T to C conversion in sequencing reads.

2021-06-25 | GSE160994 | GEO

Genetic and pharmacological evidence for kinetic competition between alternative poly(A) sites in yeast - 4tU cordycepin treatment

Project description:mPAT approach using an anchored oligo-dT (TV12VN) primer to determine changes to 3'UTR length in yeast upon cordycepin treatment and new transcription using 4-thiouracil (4tU) labelling of RNA. This appears as a T to C conversion in sequencing reads.

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Genetic and pharmacological evidence for kinetic competition between alternative poly(A) sites in yeast - 4tU cordycepin treatment

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Genetic and pharmacological evidence for kinetic competition between alternative poly(A) sites in yeast - cordycepin treatment

Project description:PAT-seq approach was used to determine changes to 3'UTR length in yeast upon addition of 20µg/ml cordycepin (3'deoxyadenosine) for 0, 5, 10, 20 or 40 minutes

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Genetic and pharmacological evidence for kinetic competition between alternative poly(A) sites in yeast - cordycepin treatment

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The molecular effects of cordycepin on RNA synthesis in Saccharomyces cerevisiae

Project description:Cordycepin (3â deoxyadenosine) is a biologically active compound that, when incorporated during RNA synthesis in vitro, provokes chain termination due to the absence of a 3â 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 3â 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 3â 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 Each experiment was performed as triplicate. We analyzed RNA obtained from wild-type cells, from wild-type cells treated with 40 microgram/ml cordycepin for 1 hour, from pap1-1 mutant cells grown at permissive temperature (25Â°C) and from pap1-1 mutant cells grown at permissive temperature (25Â°C) treated with 40 microgram/ml cordycepin for 1 hour.

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KINETIC AND COMPOSITIONAL ANALYSIS OF RNA POLYMERASE II IN TRYPANOSOMA BRUCEI

Project description:Genome-wide analysis of nascent RNA synthesis gives kinetic information on the transcriptional status of RNA polymerase II (Pol II). In parallel, immunoprecipitation of the largest subunit of Pol II (RPB1) provides the protein composition of the enzyme complex in the presence or absence of the transcriptional inhibitor Actinomycin D.

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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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Project description:Cordycepin, a 3-deoxyadenosine, a traditional Chinese medicine. Studies have demonstrated that cordycepin could modulate multiple signaling pathways to induce cancer cell death. This study aims to determine the genes regulated by Cordycepin and clarify the possible molecular mechanism underlying their action.

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Total and 4-thiouracil (4tU) labeled RNA samples of wild-type Schizosaccharomyces pombe strain ED666 (BIONEER)

Project description:RNA-seq of S.pombe total and metabolically labeled (4tU) RNA fractions with independent biological replicates. 4tU-labeling allows the isolation of newly transcribed RNAs. Samples differ in the duration of exposure with 4tU (2,4,6,8,10 minutes). For a detailed description of the labeling protocol see Miller et al. (MSB, 2011) and Schulz et al. (Cell, 2014).

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