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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Analysis of the effect of the deletion of PUF3 gene in yeast

ABSTRACT: The Puf family of RNA-binding proteins regulate gene expression by controlling protein synthesis or stimulating RNA decay. Puf3p is one of six related proteins in Saccharomyces cerevisiae characterised as targeting and regulating decay of nuclear-encoded mRNAs specifying mitochondrial proteins. Much prior work has examined how Puf3p regulates COX17 mRNA. We undertook a genome-wide approach to quantitatively assess the impact of loss of PUF3 on gene expression. Comparing transcript levels in wild-type and puf3∆ cells revealed that that only a small fraction of mRNA levels alter, suggesting Puf3p determines mRNA stability for only some target mRNAs.

INSTRUMENT(S): AB SOLiD 4 System

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: David Talavera

PROVIDER: E-MTAB-3407 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Analysis of the effect of PUF3 deletion in mRNA translation in yeast

Project description:The Puf family of RNA-binding proteins regulates gene expression by controlling protein synthesis or stimulating RNA decay. Puf3p is one of six related proteins in Saccharomyces cerevisiae characterised as targeting and regulating decay of nuclear-encoded mRNAs specifying mitochondrial proteins. Much prior work has examined how Puf3p regulates COX17 mRNA. We undertook a genome-wide approach to quantitatively assess the impact of loss of PUF3 on gene expression using polysome profiling. Our translatomic study suggests that loss of Puf3p has widespread, but modest, impact on mRNA translation.

2016-03-31 | E-MTAB-3406 | biostudies-arrayexpress

Proteomics analysis of the effect of deletion of PUF3 on yeast via LC-MSMS.

Project description:The Puf family of RNA-binding proteins regulate the expression of genes by controlling protein synthesis or stimulating RNA decay. Puf3p is one of six Puf-family members in Saccharomyces cerevisiae. Puf3p has been characterised previously as regulating mRNA decay of nuclear mRNAs that encode for mitochondrial proteins. We undertook a series of genome wide approaches to identify an expanded set of Puf3p target mRNAs and to quantitatively assess the impact of loss of PUF3 on the expression control in actively growing wild type and puf3Δ strains. Here we report our quantifications of relative protein levels. The data suggest that loss of Puf3p only impacts on a small proportion of the proteins encoded by its mRNA targets.

2016-04-13 | PXD001903 | Pride

Analysis of the role of yeast Puf3p in translation control

Project description:The Puf family of RNA-binding proteins regulate gene expression by controlling protein synthesis or stimulating RNA decay. Puf3p is one of six related proteins in Saccharomyces cerevisiae characterised as targeting and regulating decay of nuclear-encoded mRNAs specifying mitochondrial proteins. Much prior work has examined how Puf3p regulates COX17 mRNA. We undertook genome-wide approaches to define an expanded set of Puf3p target mRNAs. In agreement with prior studies, our sequencing of affinity-purified Puf3p-TAP associated mRNAs (RIP-seq) identified mRNAs encoding mitochondrially-targeted proteins. We also found an additional 720 mRNA targets that predominantly encode proteins that enter the nucleus.

2016-03-31 | E-MTAB-3413 | biostudies-arrayexpress

Analysis of the role of yeast Slf1p in translation of specific mRNAs during oxidative stress response

Project description:The mechanisms by which RNA-binding proteins control the translation of subsets of mRNAs are not yet clear. Slf1p is an atypical La motif containing protein (LARP). LARPs are members of a superfamily of RNA-binding proteins conserved across eukaryotes. We performed transcriptomics and RIP-Seq analysis in order to explore the effect of Slf1 on the amount of mRNA of genes involved in the response to oxidative stress.

2015-05-01 | E-MTAB-2567 | biostudies-arrayexpress

Analysis of the role of yeast Sro9p in controlling the translation of specific mRNAs

Project description:The mechanisms by which RNA-binding proteins control the translation of subsets of mRNAs are not yet clear. Sro9p is an atypical La motif containing protein (LARP). LARPs are members of a superfamily of RNA-binding proteins conserved across eukaryotes. We performed transcriptomics and RIP-Seq analysis in order to explore the role of Sro9 on controlling translation of genes in yeast.

2015-05-01 | E-MTAB-2568 | biostudies-arrayexpress

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

Potential modulation of Puf3 chromatin association mediated by Rpb4

2022-11-09 | GSE152093 | GEO

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

Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast

Project description:Abstract: Genes encoding RNA-binding proteins are diverse and abundant in eukaryotic genomes. Although some have been shown to have roles in post-transcriptional regulation of the expression of specific genes, few of these proteins have been studied systematically. We have used an affinity tag to isolate each of the five members of the Puf family of RNA-binding proteins in Saccharomyces cerevisiae and DNA microarrays to comprehensively identify the associated mRNAs. Distinct groups of 40-220 different mRNAs with striking common themes in the functions and subcellular localization of the proteins they encode are associated with each of the five Puf proteins: Puf3p binds nearly exclusively to cytoplasmic mRNAs that encode mitochondrial proteins; Puf1p and Puf2p interact preferentially with mRNAs encoding membrane-associated proteins; Puf4p preferentially binds mRNAs encoding nucleolar ribosomal RNA-processing factors; and Puf5p is associated with mRNAs encoding chromatin modifiers and components of the spindle pole body. We identified distinct sequence motifs in the 3'-untranslated regions of the mRNAs bound by Puf3p, Puf4p, and Puf5p. Three-hybrid assays confirmed the role of these motifs in specific RNA-protein interactions in vivo. The results suggest that combinatorial tagging of transcripts by specific RNA-binding proteins may be a general mechanism for coordinated control of the localization, translation, and decay of mRNAs and thus an integral part of the global gene expression program. This SuperSeries is composed of the SubSeries listed below.

2006-03-08 | GSE4393 | GEO

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