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Genome-wide chromosomal associationof Upf1 is linked toPol II transcriptionin Schizosaccharomyces pombe

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Schizosaccharomyces pombe

PROVIDER: GSE169425 | GEO | 2021/03/24

REPOSITORIES: GEO

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Genome-wide chromosomal association of Upf1 is linked to Pol II transcription in Schizosaccharomyces pombe.

Project description:Although the RNA helicase Upf1 has hitherto been examined mostly in relation to its cytoplasmic role in nonsense mediated mRNA decay (NMD), here we report high-throughput ChIP data indicating genome-wide association of Upf1 with active genes in Schizosaccharomyces pombe. This association is RNase sensitive, correlates with Pol II transcription and mRNA expression levels. Changes in Pol II occupancy were detected in a Upf1 deficient (upf1Δ) strain, prevalently at genes showing a high Upf1 relative to Pol II association in wild-type. Additionally, an increased Ser2 Pol II signal was detected at all highly transcribed genes examined by ChIP-qPCR. Furthermore, upf1Δ cells are hypersensitive to the transcription elongation inhibitor 6-azauracil. A significant proportion of the genes associated with Upf1 in wild-type conditions are also mis-regulated in upf1Δ. These data envisage that by operating on the nascent transcript, Upf1 might influence Pol II phosphorylation and transcription.

| S-EPMC8754637 | biostudies-literature

Genome-wide chromosomal associationof Upf1 is linked toPol II transcriptionin Schizosaccharomyces pombe [ChIP-Seq]

Project description:Although the RNA helicase Upf1 has hitherto been examined mostly in relation to its cytoplasmic role in nonsense mediated mRNA decay (NMD), here we report high-throughput ChIP data indicating genome-wide association of Upf1 with active genes in Schizosaccharomyces pombe. This association is RNase sensitive and it correlates with Pol II transcription and mRNA expression levels. Changes in Pol II occupancy were detected at only some genes in a Upf1-deficient (upf1strain, however there is an increased Ser2 Pol II signal at all highly transcribed genes examined by ChIP-qPCR. Furthermore, upf1cells are hypersensitive to the transcription elongation inhibitor 6-azauracil and display Pol II abnormalities suggestive of hyperphosphorylation. A significant proportion of the genes associated with Upf1 in wild-type conditions are also mis-regulated in upf1. These data predict that via association with the nascent transcript Upf1 might influence Pol II phosphorylation and transcription as well as mRNA processing of multiple genes.

2021-03-24 | GSE169424 | GEO

Genome-wide chromosomal associationof Upf1 is linked toPol II transcriptionin Schizosaccharomyces pombe [ChIP-chip]

Project description:Although the RNA helicase Upf1 has hitherto been examined mostly in relation to its cytoplasmic role in nonsense mediated mRNA decay (NMD), here we report high-throughput ChIP data indicating genome-wide association of Upf1 with active genes in Schizosaccharomyces pombe. This association is RNase sensitive and it correlates with Pol II transcription and mRNA expression levels. Changes in Pol II occupancy were detected at only some genes in a Upf1-deficient (upf1strain, however there is an increased Ser2 Pol II signal at all highly transcribed genes examined by ChIP-qPCR. Furthermore, upf1cells are hypersensitive to the transcription elongation inhibitor 6-azauracil and display Pol II abnormalities suggestive of hyperphosphorylation. A significant proportion of the genes associated with Upf1 in wild-type conditions are also mis-regulated in upf1. These data predict that via association with the nascent transcript Upf1 might influence Pol II phosphorylation and transcription as well as mRNA processing of multiple genes.

2021-03-24 | GSE169422 | GEO

Genome-wide chromosomal associationof Upf1 is linked toPol II transcriptionin Schizosaccharomyces pombe

Project description:Genome-wide chromosomal associationof Upf1 is linked toPol II transcriptionin Schizosaccharomyces pombe

| PRJNA716551 | ENA

Genome-wide chromosomal associationof Upf1 is linked toPol II transcriptionin Schizosaccharomyces pombe [ChIP-Seq]

Project description:Genome-wide chromosomal associationof Upf1 is linked toPol II transcriptionin Schizosaccharomyces pombe [ChIP-Seq]

| PRJNA716559 | ENA

Genome-wide chromosomal associationof Upf1 is linked toPol II transcriptionin Schizosaccharomyces pombe [ChIP-chip]

Project description:Genome-wide chromosomal associationof Upf1 is linked toPol II transcriptionin Schizosaccharomyces pombe [ChIP-chip]

| PRJNA716557 | ENA

Functional characterization of Upf1 targets in Schizosaccharomyces pombe.

Project description:Nonsense-mediated mRNA decay (NMD) is a highly conserved mechanism of mRNA degradation. NMD eliminates mRNAs containing premature termination codons (PTCs), preventing the production of truncated proteins with possible deleterious effects. However, there is mounting evidence that NMD factors, like Upf1, Upf2 and Upf3, participate in general regulation of gene expression, affecting the expression of genes lacking PTCs. We have used the fission yeast Schizosaccharomyces pombe to identify mRNAs directly regulated by NMD. Using a combination of genetic and biochemical approaches, we have defined a population of fission yeast mRNAs specifically regulated by Upf1. We show that other components of the Upf complex, Upf2 and Upf3, are required for binding of Upf1 to its RNA targets and for the proper response of fission yeast to oxidative stress. Finally, we investigated the physiological importance of this phenomenon, and demonstrate that the Upf1-dependent downregulation of some of its direct targets is necessary for normal resistance to oxidative stress.

| S-EPMC3904585 | biostudies-literature