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

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

PROVIDER: PRJNA638297 | ENA |

REPOSITORIES: ENA

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

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. 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.

2022-11-09 | GSE152094 | GEO

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

Project description:Gene expression involving RNA polymerase II is regulated by the concerted interplay between mRNA synthesis and degradation, crosstalk in which mRNA decay machinery and transcription machinery respectively impact transcription and mRNA stability. Rpb4, and likely dimer Rpb4/7, seem the central components of the RNA pol II governing these processes. In this work we unravel the molecular mechanisms participated by Rpb4 that mediate the posttranscriptional events regulating mRNA imprinting and stability. By RIP-Seq, we analysed genome-wide the association of Rpb4 with mRNAs and demonstrated that it targeted a large population of more than 1400 transcripts. A group of these mRNAs was also the target of the RNA binding protein, Puf3. We demonstrated that Rpb4 and Puf3 physically, genetically, and functionally interact and also affect mRNA stability, and likely the imprinting, of a common group of mRNAs. Furthermore, the Rpb4 and Puf3 association with mRNAs depends on one another. We also demonstrated, for the first time, that Puf3 associates with chromatin in an Rpb4-dependent manner. Our data also suggest that Rpb4 could be a key element of the RNA pol II that coordinates mRNA synthesis, imprinting and stability in cooperation with RBPs.

| S-EPMC8244751 | biostudies-literature

Rpb4 and Puf3

Project description:Rpb4 and Puf3

| PRJNA638290 | ENA

Potential modulation of Puf3 chromatin association mediated by Rpb4

2022-11-09 | GSE152093 | GEO

Potential modulation of Puf3 chromatin association mediated by Rpb4

Project description:Potential modulation of Puf3 chromatin association mediated by Rpb4

| PRJNA638298 | ENA

Pbp1 associates with Puf3 and promotes translation of its target mRNAs involved in mitochondrial biogenesis

Project description:Pbp1 (polyA-binding protein - binding protein 1) is a stress granule marker and polyglutamine expansions in its mammalian ortholog ataxin-2 have been linked to neurodegenerative conditions. Pbp1 was recently shown to form intracellular assemblies that function in the negative regulation of TORC1 signaling under respiratory conditions. Furthermore, it was observed that loss of Pbp1 leads to mitochondrial dysfunction. Here, we show that loss of Pbp1 leads to a specific decrease in mitochondrial proteins whose encoding mRNAs are targets of the RNA-binding protein Puf3, suggesting a functional relationship between Pbp1 and Puf3. We found that Pbp1 stabilizes and promotes the translation of Puf3-target mRNAs in respiratory conditions, such as those involved in the assembly of cytochrome c oxidase. We further show that Pbp1 and Puf3 associate through their respective low complexity domains, which is required for target mRNA stabilization and translation. Our findings reveal a key role for Pbp1-containing assemblies in enabling the translation of mRNAs critical for mitochondrial biogenesis and respiration under metabolically challenging conditions. They may further explain prior associations of Pbp1/ataxin-2 with stress granule biology and RNA metabolism.

2023-05-08 | GSE227356 | GEO

Schizosaccharomyces pombe Puf3 interactome

Project description:Puf3 is a RNA-binding protein, a member of the conserved Puf-protein family. Combining different functional genomics data, we have analyzed the role of Puf3 in post-transcriptional gene regulation in S. pombe. We present data on Puf3 interacting proteins and regulatory mRNA targets.

2022-03-23 | PXD006318 | Pride

Identification of RNAs associated with S. cerevisiae or N. crassa Puf3

Project description:Affinity purification of S. cerevisiae or N. crassa Puf3 from S. cerevisiae cells and identification of associated RNAs by microarray

2015-03-16 | GSE50996 | GEO

PUF3 RNAi in bloodstream-form trypanosomes

Project description:PUF3 was depleted by RNAi for 24h in bloodstream-form trypanosomes (Trypanosoma brucei). No effect was seen on the transcriptome.

2019-06-30 | E-MTAB-8062 | biostudies-arrayexpress

PUF3 RIP and rRNA depletion control

Project description:Cells expressing Tap-Tagged PUF3 were used for selection on IgG beads, then released using TEV protease. Samples were input and bound fraction without rRNA removal, and unbound fraction and input after rRNA removal with oligonucleotides and RNase H.

2019-06-28 | E-MTAB-8068 | biostudies-arrayexpress

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