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Rpb4 and Puf3 imprint and post-transcriptionally control stability of a common set of mRNAs in yeast

ABSTRACT: Gene expression involving RNA polymerase II is regulated by the concerted interplay between mRNA synthesis and degradation, a crosstalk where mRNA decay machinery impacts transcription and transcription machinery influences mRNA stability. Rpb4, and likely the dimer Rpb4/7 seem to be the central components of the RNA pol II governing these processes. In this work we unravel more precisely the molecular mechanisms participated by Rpb4 that mediates the posttranscriptional events regulating mRNA imprinting and stability. We analysed genome-wide, by RIP-seq, the association of Rpb4 with mRNAs and demonstrated that it targets a broad population of about 1400 transcripts. A group of mRNAs are also targets of the RPB, Puf3. We demonstrated that Rpb4 and Puf3, physically, genetically and functionally interact and cooperate to imprint and regulate stability of this group of mRNA. We also demonstrated, by the first time, that Puf3 associates with the chromatin, in an Rpb4-dependent manner. Our data also point to Rpb4 as the key element of the RNA pol II that interplay mRNA synthesis, imprinting and stability, in cooperation with RBPs.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE152094 | GEO | 2022/11/09

REPOSITORIES: GEO

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Potential modulation of Puf3 chromatin association mediated by Rpb4

Project description:Gene expression involving RNA polymerase II is regulated by the concerted interplay between mRNA synthesis and degradation, a crosstalk where mRNA decay machinery impacts transcription and transcription machinery influences mRNA stability. Rpb4, and likely the dimer Rpb4/7 seem to be the central components of the RNA pol II governing these processes. Here we investigate the effect of ∆rrp4 on the potential chromatin association of the RNA binding protein Puf3 to chromatin in S. cerevisiae.

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Genome-associated RNA Polymerase II includes the dissociable Rpb4/7 subcomplex

Project description:Yeast RNA polymerase (Pol) II consists of a ten-subunit core enzyme and the Rpb4/7 subcomplex, which is dispensable for catalytic activity and dissociates in vitro. To investigate whether Rpb4/7 is an integral part of DNA-associated Pol II in vivo, we used chromatin immuno-precipitation coupled to high-resolution tiling microarray analysis. We show that the genome-wide occupancy profiles for Rpb7 and the core subunit Rpb3 are essentially identical. Thus, the complete Pol II associates with DNA in vivo, consistent with functional roles of Rpb4/7 throughout the transcription cycle. Keywords: ChIP-chip Comparison of Rpb3 vs. Rpb4/7 genome-wide occupancy profiles. Data obtained from independent ChIP-chip experiments on two yeast strains: S288C Rpb3TAP vs. Rpb7-TAP strain and W303 Rpb3-TAP vs. wild type strain (IP with the monoclonal antibody for Rpb4/7). Biological replicates W303 strains: 1 x Rpb3-TAP, 1 x wt with Rpb4/7 antibody, independently grown and harvested. Biological replicates S288C strains: 3 x Rpb3-TAP, 2 x Rpb7-TAP, independently grown and harvested. One replicate per array.

2008-07-29 | E-GEOD-12060 | biostudies-arrayexpress

The transcription factor Sfp1 imprints specific classes of mRNAs and links their synthesis and cytoplasmic decay

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