Saccharomyces cerevisiae
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA396583 | ENA |
REPOSITORIES: ENA
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Project description:Nonsense-mediated mRNA decay (NMD) is a major translation-dependent RNA degradation pathway required for embryo development and telomere maintenance. Core NMD factors Upf1, Upf2 and Upf3 are conserved from yeast to mammals but a model of the NMD machinery compatible with all eukaryotes is not yet available. We performed the first large-scale quantitative characterization of yeast NMD complexes through affinity purification and mass-spectrometry with 7 different NMD-related factors, with or without Rnase, in strains deleted or not for NMD genes. This extensive characterization of NMD complexes identified two distinct complexes associated with Upf1: Detector (Upf1/2/3) and Effector. Effector contained, in addition to Upf1, the mRNA decapping enzyme and two potential equivalents of mammalian Smg6/5/7: Nmd4 and Ebs1. Like the Smg proteins, Nmd4 and Ebs1 were required for efficient NMD. Our results suggest that the core eukaryotic NMD machinery is conserved across species and operates through successive Upf1-bound Detector and Effector complexes.
2018-03-12 | PXD007159 | Pride
Project description:A High Resolution Profile of NMD Substrates in Yeast
| PRJNA341846 | ENA
Project description:MNase-sensitive complexes in yeast: nucleosomes and non-histone barriers
| PRJNA324842 | ENA
Project description:System level characterization of galactose mutants of yeast
| PRJNA137359 | ENA
Project description:The yeast and human FACT complexes resolve R-loop-mediated transcription-replication conflicts
| PRJNA224239 | ENA
Project description:Using RNA-Seq analysis of nonsense-mediated mRNA decay (NMD) mutant strains, we show that many Saccharomyces cerevisiae intron-containing genes exhibit usage of alternative splice sites, but most transcripts generated by splicing from these sites are non-functional because they introduce premature termination codons leading to transcript degradation by NMD. Analysis of splicing mutants combined with NMD inactivation revealed the role of specific splicing factors in governing the use of these alternative splice sites and identified novel functions for Prp17p in enhancing the use of branchpoint-proximal upstream 3M-bM-^@M-^Y splice sites and for Prp18p in suppressing the usage of a non-canonical AUG 3M-bM-^@M-^Y-splice site. The use of non-productive alternative splice sites can limit the expression of some transcripts and can be increased in stress conditions in a promoter-dependent manner, contributing to the down-regulation of genes during stress. These results reveal that alternative splicing is frequent in S.cerevisiae but masked by RNA degradation and that the use of alternative splice sites is mostly aimed at controlling transcript levels rather than increasing proteome diversity. mRNA-Seq profiling of 3 mutants in the nonsense-mediated mRNA decay pathway and wildtype yeast
2014-02-21 | E-GEOD-55213 | biostudies-arrayexpress
Project description:The aim of present study is to understand the impact of genetic engineering event, integration of ClCBH2 gene into yeast genome, as well as the subsequent biological process, such as expression and secretion of CBH2 protein. Further, the ‘dosage’ of genetic engineering event, the copy number inserted ClCBH2 gene, is also of particular interest. In parallel, the relationship between the copy number of ClCBH2 gene and the condition of yeast culture during CBH2 production, as well as the effect of these two factors towards yeast metabolism are investigated. Extensive transcriptomics analysis and comparison were conducted for three CBP yeast strains with different copy numbers of ClCBH2 gene, at two growth rates
2015-08-27 | GSE72413 | GEO
Project description:Molecular characterization of baker's yeast
| PRJEB29240 | ENA
Project description:The goal of this set of experiments was to identify transcripts that are differentially expressed upon reactivation of NMD in an nmd2::HIS3 strain by galactose-induced expression of the NMD2 gene. Experiment Overall Design: Yeast strains harboring nmd2::HIS3 and the GAL1-NMD2 allele on a plasmid or the empty vector were grown in SC-medium containing raffinose but lacking uracile. Genome-wide expression profiles of the GAL-NMD2 and nmd2 deletion strains were analyzed over a 60-minute time course after adding galactose to the cell cultures. Four independent replicates were carried out for this experiment.
2008-06-16 | E-GEOD-9482 | biostudies-arrayexpress
Project description:The vast landscape of RNA-protein interactions at the heart of post-transcriptional regulation remains largely unexplored. Indeed it is likely that, even in yeast, a substantial fraction of the regulatory RNA-binding proteins (RBPs) remain to be discovered. Systematic experimental methods can play a key role in discovering these RBPs - most of the known yeast RBPs lack RNA-binding domains that might enable this activity to be predicted. We describe here a new proteome-wide approach to identify RNA-protein interactions based on in vitro binding of RNA samples to yeast protein microarrays that represent over 80% of the yeast proteome. We used this procedure to screen for novel RBPs and RNA-protein interactions. A complementary mass spectrometry technique also identified proteins that associate with yeast mRNAs. Both the protein microarray and mass spectrometry methods successfully identify previously annotated RBPs, suggesting that other proteins identified in these assays might be novel RBPs. Of 35 putative novel RBPs identified by either or both of these methods, 12, including 75% of the eight most highly-ranked candidates, reproducibly associated with specific cellular RNAs. Surprisingly, most of the 12 newly discovered RBPs were enzymes. Functional characteristics of the RNA targets of some of the novel RBPs suggest coordinated post-transcriptional regulation of subunits of protein complexes and a possible link between mRNA trafficking and vesicle transport. Our results suggest that many more RBPs still remain to be identified and provide a set of candidates for further investigation.
2011-03-10 | GSE22876 | GEO