Saccharomyces cerevisiae
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA230517 | ENA |
REPOSITORIES: ENA
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Project description:Eukaryotic cells have to prevent the export of unspliced pre-mRNAs until intron removal is completed to avoid the expression of aberrant and potentially harmful proteins. Only mature RNAs associate with the export receptor Mex67 (mammalian TAP) and enter the cytoplasm. The underlying nuclear quality control mechanisms are still unclear. Here we show that two shuttling SR-proteins Gbp2 and Hrb1 are key surveillance factors for the selective export of spliced mRNAs in yeast. Their absence leads to the significant leakage of unspliced pre-mRNAs into the cytoplasm. They bind to pre-mRNAs and the spliceosome during splicing, where they are necessary for the surveillance of splicing and the stable binding of the TRAMP-complex to the spliceosome-bound transcripts. Faulty transcripts are marked for their degradation at the nuclear exosome. On correct mRNAs the SR-proteins recruit Mex67 upon completion of splicing to allow a quality controlled nuclear export. Altogether, these data identify a role for shuttling SR-proteins in mRNA surveillance and nuclear mRNA quality control. 6 samples, i.e. 2 replicates per protein Gbp2, Hrb1 and Npl3
2013-12-04 | E-GEOD-52808 | biostudies-arrayexpress
Project description:Eukaryotic cells have to prevent the export of unspliced pre-mRNAs until intron removal is completed to avoid the expression of aberrant and potentially harmful proteins. Only mature RNAs associate with the export receptor Mex67 (mammalian TAP) and enter the cytoplasm. The underlying nuclear quality control mechanisms are still unclear. Here we show that two shuttling SR-proteins Gbp2 and Hrb1 are key surveillance factors for the selective export of spliced mRNAs in yeast. Their absence leads to the significant leakage of unspliced pre-mRNAs into the cytoplasm. They bind to pre-mRNAs and the spliceosome during splicing, where they are necessary for the surveillance of splicing and the stable binding of the TRAMP-complex to the spliceosome-bound transcripts. Faulty transcripts are marked for their degradation at the nuclear exosome. On correct mRNAs the SR-proteins recruit Mex67 upon completion of splicing to allow a quality controlled nuclear export. Altogether, these data identify a role for shuttling SR-proteins in mRNA surveillance and nuclear mRNA quality control.
2013-12-04 | GSE52808 | GEO
Project description:Three shuttling SR-like proteins exist in Saccharomyces cerevisiae, Npl3, Gbp2 and Hrb1, that are involved in the nuclear export of mRNAs. In a screen for genes that regulate the export of Gbp2, we identified novel mutants of the splicing factors PRP8 and PRP17 that lead to severe mislocalization defects for Gbp2 and Hrb1, but not Npl3. Microarray and qRT-PCR analyses show that Gbp2 and Hrb1 preferentially bind to transcripts derived from intron-containing genes. Moreover, in contrast to Npl3, Gbp2 and Hrb1 show genetic and physical interactions with late splicing factors such as Prp17 and Prp43. Further, RNA co-immunoprecipitation experiments reveal that, unlike Npl3, association of Gbp2 and Hrb1 with the mRNA requires splicing, and this in turn is required for their Mex67 recruitment. We propose a model in which Gbp2 and Hrb1 are attached to the mRNAs at late stages of splicing to promote the subsequent export of spliced mRNAs. keyword: RIP-chip RNA-IP of endogenously expressed 3-fold C-terminal myc-tagged Gbp2 and Hrb1 in S288C background cells was each performed once in cells grown to a density of 4x10^7 cells/ml and hybridized against a total (input) RNA reference.
2013-08-30 | E-GEOD-20738 | biostudies-arrayexpress
Project description:Spliced messages constitute one-fourth of expressed mRNAs in the yeast Saccharomyces cerevisiae, and most mRNAs in metazoans. Splicing requires 5' splice site (5'SS), branch point (BP), and 3' splice site (3'SS) elements, but the role of the BP in splicing control is poorly understood because BP identification remains difficult. We developed a high-throughput method, Branch-seq, to map BP and 5'SS of isolated RNA lariats. Applied to S. cerevisiae, Branch-seq detected 76% of expressed, annotated BPs and identified a comparable number of novel BPs. We used RNA-seq to confirm associated 3'SS locations, identifying some 200 novel splice junctions, including an AT-AC intron. We show that several yeast introns use two or even three different BPs, with effects on 3'SS choice, protein coding potential, or RNA stability and identify novel introns whose splicing changes during meiosis or in response to stress. Together, these findings reveal BP-based regulation and demonstrate unanticipated complexity of splicing in yeast.
2016-08-01 | GSE68022 | GEO
Project description:Cytoplasmic RNA granules compartmentalize phases of the translation cycle in eukaryotes. We previously reported the localization of oxidized RNA to cytoplasmic foci called oxidized RNA bodies (ORBs) in human cells. We show here that ORBs are RNA granules in Saccharomyces cerevisiae. Several lines of evidence support a role of ORBs in the compartmentalization of no-go decay and ribosome quality control, the translation quality control pathways that recognize and clear aberrant mRNAs, including those with oxidized bases. Translation is required by these pathways and ORBs. Translation quality control factors localize to ORBs. A substrate of translation quality control, a stalled mRNA-ribosome-nascent chain complex, localizes to ORBS. Translation quality control mutants have altered ORB numbers, sizes, or both. In addition, we identify 68 ORB proteins, by immunofluorescence staining directed by proteomics, which further support their role in translation quality control and reveal candidate new factors for these pathways.
2022-11-23 | PXD037184 | Pride
Project description:Spliced messages constitute one-fourth of expressed mRNAs in the yeast Saccharomyces cerevisiae, and most mRNAs in metazoans. Splicing requires 5' splice site (5'SS), branch point (BP), and 3' splice site (3'SS) elements, but the role of the BP in splicing control is poorly understood because BP identification remains difficult. We developed a high-throughput method, Branch-seq, to map BP and 5'SS of isolated RNA lariats. Applied to S. cerevisiae, Branch-seq detected 76% of expressed, annotated BPs and identified a comparable number of novel BPs. We used RNA-seq to confirm associated 3'SS locations, identifying some 200 novel splice junctions, including an AT-AC intron. We show that several yeast introns use two or even three different BPs, with effects on 3'SS choice, protein coding potential, or RNA stability and identify novel introns whose splicing changes during meiosis or in response to stress. Together, these findings reveal BP-based regulation and demonstrate unanticipated complexity of splicing in yeast. 1 Lariat-seq experiment library. 3 barcoded Branch-seq libraries that make up one experiment. 26 RNA-seq samples, 2 biological replicates of each.
2016-08-01 | E-GEOD-68022 | biostudies-arrayexpress
Project description:Oxidative quality control regulates response to ER stress through translation control
| PRJNA281482 | ENA
Project description:Ubiquitination of Stalled Ribosome Triggers Ribosome-associated Quality Control [SET1]
| PRJNA316463 | ENA
Project description:Ubiquitination of Stalled Ribosome Triggers Ribosome-associated Quality Control [SET2]
| PRJNA356354 | ENA
Project description:Translation elongation mediated quality control of integral membrane protein synthesis
| PRJNA302167 | ENA