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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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

ABSTRACT: 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.

INSTRUMENT(S): AB SOLiD 4 System

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: David Talavera

PROVIDER: E-MTAB-2568 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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The yeast La related protein Slf1p is a key activator of translation during the oxidative stress response.

Kershaw Christopher J CJ Costello Joseph L JL Castelli Lydia M LM Talavera David D Rowe William W Sims Paul F G PF Ashe Mark P MP Hubbard Simon J SJ Pavitt Graham D GD Grant Chris M CM

PLoS genetics 20150108 1

The mechanisms by which RNA-binding proteins control the translation of subsets of mRNAs are not yet clear. Slf1p and Sro9p are atypical-La motif containing proteins which are members of a superfamily of RNA-binding proteins conserved in eukaryotes. RIP-Seq analysis of these two yeast proteins identified overlapping and distinct sets of mRNA targets, including highly translated mRNAs such as those encoding ribosomal proteins. In paralell, transcriptome analysis of slf1Δ and sro9Δ mutant strains ...[more]

PMID: 25569619

Similar Datasets

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 effect of the deletion of PUF3 gene in yeast

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 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.

2016-03-31 | E-MTAB-3407 | biostudies-arrayexpress

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 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

RIP-seq of Saccharomyces cerevisiae to identify RNAs which associate with members of the closed loop complex (eIF4E, eIF4GI, eIF4GII, Pab1p) and inhibtors of the complex (Caf20p, Eap1p)

Project description:The aim of this experiment was to look at RNAs which associate with members of the closed loop complex (eIF4E, eIF4GI, eIF4GII, Pab1p) and inhibtors of the complex (Caf20p, Eap1p) under optimal growth conditions in the Saccharomyces cerevisiae BY4741 strain background. NOTE: The csfasta and qual files associated with sample eIF4G1-IP(1) (ERS435094) were changed on 17th October 2014 and a new run accession assigned to the new files (ERR657892).

2014-08-01 | E-MTAB-2464 | biostudies-arrayexpress

Analysis of the effect of the farnesol on transcript levels and polysome association in C. albicans

Project description:Farnesol is a quorum-sensing sesquiterpene alcohol that, via regulation of specific signalling and transcription components, inhibits filamentous growth in Candida. We have found that farnesol also inhibits translation at the initiation step. In contrast to fusel alcohols, that target the eukaryotic initiation factor 2B (eIF2B), farnesol affects the interaction of the mRNA with the small ribosomal subunit leading to reduced levels of the 48S pre-ribosomal complex. To establish the impact of farnesol and how effects on transcription and translation might be co-ordinated, we identified farnesol-dependent changes at both the transcript level and at the level of polysome association using next generation sequencing approaches.

2016-07-31 | E-MTAB-3843 | biostudies-arrayexpress

Pervasive genomic transcription during oxidative stress generates thousands of previously uncharacterized lncRNAs (RNA-Seq)

Project description:Oxidative stress (OS) is caused by an imbalance between pro-oxidant and antioxidant reactions which leads to accumulation of reactive oxygen species (ROS) within cells. ROS can be harmful, due to their damaging effects on several cellular components, but are at the same time essential components of signaling cues. We investigate the effect of OS on the immediate early transcriptional response at a genomic level, by deep sequencing of nuclear and cytosolic RNA fractions, in in human fibroblasts treated for 30 or 120 minutes with sub-lethal doses of H2O2. In contrast to most of the protein-coding transcriptome, OS induces de novo transient transcription of thousands of previously uncharacterized genomic loci. We classify these stress induced long non coding RNAs (lncRNA) based on their genomic annotation and strand orientation relative to their nearest gene: distal, overlapping, terminal-associated or promoter-associated. The latter class of stress-induced promoter associated antisense lncRNAs (si-paancRNAs), is preferentially transcribed by PolII, which elongates from bidirectional promoters, enriched for specific transcription factor-binding sites (ZFP161, ZFX, MEF2A and divergent-FOS motives). Interestingly the associated sense-coding genes belong to specific functional categories (cellular response to stress and others). We finally demonstrate that a subset of si-paancRNAs associate better with the translation machinery, which is stalled, upon OS. Most studies to date have focused on the repertoire of lncRNAs present in physiological conditions. We here report the surprising result that thousands of lncRNAs are transcriptionally upregulated upon OS from specific loci possibly playing a role in physiological or pathological response to stress. RNA-Sequencing profiles of nuclear and cytosolic fractions of fibroblast cell lines after 0, 30 and 120 minutes of treatment with H2O2.

2015-05-27 | E-GEOD-55169 | biostudies-arrayexpress

Transcriptional and epigenetic high throughput sequencing of human and mouse pancreatic islet-cells

Project description:The aim of this experiment was to obtain a detailed transcriptional landscape of human and mouse islet-cells, including strand information, as well an epigenetic map of transcriptionally active chromatin.

2012-10-03 | E-MTAB-1294 | biostudies-arrayexpress

Whole transcriptome of Lewis lung carcinoma cells of Mus musculus

Project description:Purpose: To study the alteration of whole transcriptome of Lewis lung carcinoma (LLC) cells after the decreasing of malignant properties of tumor by treatment of tumor-bearing mice with RNase A. Methods: Whole transcriptome profile of Lewis lung carcinoma before and after RNase A treatment were generated by deep sequencing using SOLiD 5.5. The sequence reads were mapped by Bioscope 1.3 software, differential expression was evaluated by Cufflinks v.2.0.1 package. Results: Difference in expression was found for 966 genes. Conclusions: Our study represents the first detailed analysis of alteration of transcriptome of Lewis lung carcinoma after the decrease of malignant prtoperties of the tumor (proliferation and invasion) by RNase A. Whole transcriptome profile of Lewis lung carcinoma before and after RNase A treatment were generated by deep sequencing using SOLiD 5.5.

2014-12-03 | E-GEOD-63758 | biostudies-arrayexpress

Effect of stress on the binding affinity of yeast eIF4F components to their target RNAs

Project description:Translation factors eIF4E and eIF4G form eIF4F, which binds to mRNAs to promote ribosome recruitment and translation initiation. We were interested in analysing the effects of stresses on eIF4F interactions with individual mRNAs. We used a RIP-seq approach to assess how mRNA associations with eIF4E, eIF4G1 and eIF4G2 change in response to three stresses: 1) addition of hydrogen peroxide; 2) amino acids withdrawal; and, 3) glucose withdrawal. We find that acute stress leads to changes in eIF4FmRNA interactions that are shared among each factor and across the stresses imposed.

2017-10-11 | E-MTAB-5836 | biostudies-arrayexpress

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