Genomewide Analysis of Clp1 Function in Transcription in Budding Yeast
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ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE71624 | GEO | 2017/07/31
REPOSITORIES: GEO
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Project description: Not available
| S-EPMC5537279 | biostudies-literature
Project description:The yeast mRNA export adaptor Yra1 binds the Pcf11 subunit of cleavage-polyadenylation factor CF1A linking export to 3'-end formation. We found a surprising consequence of this interaction is that Yra1 influences cleavage-polyadenylation. Yra1 competes with the CF1A subunit, Clp1, for binding to Pcf11, and excess Yra1 inhibits 3' processing in vitro. Release of Yra1 at the 3' ends of genes coincides with recruitment of Clp1, and depletion of Yra1 enhances Clp1 recruitment within some genes. These results suggest that CF1A is not necessarily recruited as a complete unit, but instead Clp1 can be incorporated co-transcriptionally in a process regulated by Yra1. Yra1 depletion causes widespread changes in poly(A) site choice particularly at sites where the efficiency element is divergently positioned. We propose that one way Yra1 modulates cleavage-polyadenylation is by influencing co-transcriptional assembly of the CF1A/B 3' processing factor. Key Words: Yra1, cleavage-polyadenylation, mRNA export, Pcf11, Clp1, Sub2, alternative polyadenylation
2011-09-25 | GSE30703 | GEO
Project description:The yeast mRNA export adaptor Yra1 binds the Pcf11 subunit of cleavage-polyadenylation factor CF1A linking export to 3'-end formation. We found a surprising consequence of this interaction is that Yra1 influences cleavage-polyadenylation. Yra1 competes with the CF1A subunit, Clp1, for binding to Pcf11, and excess Yra1 inhibits 3' processing in vitro. Release of Yra1 at the 3' ends of genes coincides with recruitment of Clp1, and depletion of Yra1 enhances Clp1 recruitment within some genes. These results suggest that CF1A is not necessarily recruited as a complete unit, but instead Clp1 can be incorporated co-transcriptionally in a process regulated by Yra1. Yra1 depletion causes widespread changes in poly(A) site choice particularly at sites where the efficiency element is divergently positioned. We propose that one way Yra1 modulates cleavage-polyadenylation is by influencing co-transcriptional assembly of the CF1A/B 3' processing factor. Key Words: Yra1, cleavage-polyadenylation, mRNA export, Pcf11, Clp1, Sub2, alternative polyadenylation
2011-09-25 | GSE30705 | GEO
Project description:The yeast mRNA export adaptor Yra1 binds the Pcf11 subunit of cleavage-polyadenylation factor CF1A linking export to 3'-end formation. We found a surprising consequence of this interaction is that Yra1 influences cleavage-polyadenylation. Yra1 competes with the CF1A subunit, Clp1, for binding to Pcf11, and excess Yra1 inhibits 3' processing in vitro. Release of Yra1 at the 3' ends of genes coincides with recruitment of Clp1, and depletion of Yra1 enhances Clp1 recruitment within some genes. These results suggest that CF1A is not necessarily recruited as a complete unit, but instead Clp1 can be incorporated co-transcriptionally in a process regulated by Yra1. Yra1 depletion causes widespread changes in poly(A) site choice particularly at sites where the efficiency element is divergently positioned. We propose that one way Yra1 modulates cleavage-polyadenylation is by influencing co-transcriptional assembly of the CF1A/B 3' processing factor. Key Words: Yra1, cleavage-polyadenylation, mRNA export, Pcf11, Clp1, Sub2, alternative polyadenylation mRNA poly (A) sites were mapped by sequencing 3' ends in WT and Yra1-depleted cells using a GAL1-YRA1 mutant. RNA seq of mRNA 3' ends using Illumina platform.
2011-09-24 | E-GEOD-30703 | biostudies-arrayexpress
Project description:The yeast mRNA export adaptor Yra1 binds the Pcf11 subunit of cleavage-polyadenylation factor CF1A linking export to 3'-end formation. We found a surprising consequence of this interaction is that Yra1 influences cleavage-polyadenylation. Yra1 competes with the CF1A subunit, Clp1, for binding to Pcf11, and excess Yra1 inhibits 3' processing in vitro. Release of Yra1 at the 3' ends of genes coincides with recruitment of Clp1, and depletion of Yra1 enhances Clp1 recruitment within some genes. These results suggest that CF1A is not necessarily recruited as a complete unit, but instead Clp1 can be incorporated co-transcriptionally in a process regulated by Yra1. Yra1 depletion causes widespread changes in poly(A) site choice particularly at sites where the efficiency element is divergently positioned. We propose that one way Yra1 modulates cleavage-polyadenylation is by influencing co-transcriptional assembly of the CF1A/B 3' processing factor. Key Words: Yra1, cleavage-polyadenylation, mRNA export, Pcf11, Clp1, Sub2, alternative polyadenylation Whole genome analysis of Yra1, Sub2, Pcf11, and Clp1 in WT and Yra1-depleted cells using a GAL1-YRA1 mutant. ChiP-ChIP using ligation-mediated PCR amplified material hybridized to Nimblegen 385K arrays 50mers median probe spacing 32 bp cat. No. C4214-00-01.
2011-09-24 | E-GEOD-30705 | biostudies-arrayexpress
Project description:Schizosaccharomyces pombe Clp1 is a Cdc14-family phosphatase that reverses mitotic Cdk1 phosphorylation. Despite evolutionary conservation, Clp1’s mammalian orthologs do not share this function. Rather, higher eukaryotic Cdc14 enzymes act in DNA repair, ciliogenesis, and gene regulation. To examine if Clp1 regulates gene expression, we compared the transcriptional profiles of cells lacking Clp1 function to that of wildtype. Because clp1∆ cells are sensitive to the actin depolymerizing drug, LatrunculinA, we also investigated whether a transcriptional response was involved. Our results indicate that Clp1 does not detectably affect gene expression and highlight the organism-specific functions of this conserved phosphatase family.
2024-03-11 | GSE255124 | GEO
Project description:The clp1 gene is a b-regulated gene that is required for clamp formation during the biotrophic growth phase of U. maydis. Interaction studies demonstrated that Clp1 imnteracts with Rbf1, the central regulator of pathogenciity. To exclude b-dependent effects the experiments were performed in a b-null background to analyze clp1-depndent effects on rbf controlled gene regulation
2010-09-17 | GSE21121 | GEO
Project description:Clp1 promotes 3’UTR shortening and higher levels of Aire-upregulated transcripts in mTEChi
2020-05-05 | GSE140878 | GEO
Project description:The clp1 gene is a b-regulated gene that is required for clamp formation during the biotrophic growth phase of U. maydis. Interaction studies demonstrated that Clp1 imnteracts with Rbf1, the central regulator of pathogenciity. To exclude b-dependent effects the experiments were performed in a b-null background to analyze clp1-depndent effects on rbf controlled gene regulation Strains UKH156 (nitrate inducible Rbf1 expression) and UKH164 (arabinose-inducible Clp1 and and nitrate-inducible Rbf1 expression) were grown for 12h in liquid array medium/nitrate/arabinose.
2010-09-17 | E-GEOD-21121 | biostudies-arrayexpress
Project description:The clp1 gene is a b-regulated gene that is required for clamp formation during the biotrophic growth phase of U. maydis. Clp1 expression blocks b-dependent filament formation and cell cycle arrest if co-induced with the b-heterodimer.
2011-03-30 | GSE21119 | GEO