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Extensive structural differences of closely related 3’ mRNA isoforms: links to Pab1 binding and mRNA stability

ABSTRACT: Extensive structural differences of closely related 3’ mRNA isoforms: links to Pab1 binding and mRNA stability

PROVIDER: PRJNA378410 | ENA |

REPOSITORIES: ENA

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Extensive structural differences of closely related 3’ mRNA isoforms: links to Pab1 binding and mRNA stability

Project description:Alternative polyadenylation generates numerous 3' mRNA isoforms per gene; regulation of this process is critical in development and impaired in cancer. Individual isoforms from the same gene can vary greatly in biological properties such as translational efficiency, localization, and half-life. Even closely related isoforms - including those differing by a single nt - can have different biological properties, but the underlying mechanisms are unknown. Here we show that many highly similar yeast isoforms unexpectedly exhibit extensive structural variation and differential Pab1 binding, and that these physical properties serve as a good predictor of relative isoform stability. We developed DREADS, a dimethyl sulphate (DMS)-based technique, to obtain the first transcriptome-scale structural description of individual 3' mRNA isoforms in vivo. Strikingly, near-identical yeast mRNA isoforms arising from the same gene can possess dramatically different DMS modification profiles over hundreds of nt upstream of the poly(A) tail. DREADS analyses of the same mRNAs refolded in vitro or in different species indicate that structural differences in vivo are often due to trans- acting factors. CLIP-READS, a technique we developed to measure isoform-specific binding, reveals that differences in Poly(A) binding protein (Pab1) binding to 3' ends correlate with the extent of structural variation for closely-spaced isoforms. A pattern encompassing single-strandedness near the 3' terminus, double-stranded character of the poly(A) tail, and low Pab1 binding is significantly associated with mRNA stability. Sequences responsible for isoform-specific structures, differential Pab1 binding, and mRNA stability are evolutionarily conserved, and are indicative of biological function.

2018-10-11 | GSE95788 | GEO

Extensive Structural Differences of Closely Related 3' mRNA Isoforms: Links to Pab1 Binding and mRNA Stability.

Project description: Not available

| S-EPMC6289678 | biostudies-literature

Direct and indirect consequences of PAB1 deletion in the regulation of translation initiation, translation termination, and mRNA decay

Project description:Cytoplasmic poly(A)-binding protein (PABPC, yeast Pab1) is involved in various stages of mRNA post-transcriptional control, including translation initiation, translation termination, and mRNA decay regulation. Due to the multi-functional properties of PABPC, attempts to define a specific role for PABPC in vivo by deleting, depleting, overexpressing, or mutating the protein has led to conflicting models of PABPC's function. To specifically assess direct and indirect consequences of deleting PABPC, we generated and analyzed RNA-Seq, ribosome profiling, and mass spectrometry data from yeast cells lacking Pab1.

2023-06-09 | PXD041495 | Pride

Direct and indirect consequences of PAB1 deletion in the regulation of translation initiation, translation termination, and mRNA decay [Ribo-seq]

2023-05-31 | GSE229692 | GEO

Direct and indirect consequences of PAB1 deletion in the regulation of translation initiation, translation termination, and mRNA decay [RNA-seq]

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RNAs associated with Upf1, Pab1, Rpl16a, Lsm1 proteins in yeast

Project description:Nonsense mediated mRNA decay (NMD) is a translation-dependent surveillance pathway that eliminates RNAs with short open reading frames (ORFs) and long 3' untranslated regions (UTRs). Upf1 is the key protein of this degradation pathway and we were interested to purify the associated RNAs. Moreover we have done purifications of two proteins from the general mRNA turnover in yeast : Pab1 and Lsm1 that both bind RNAs poly(A) tails. We have also done a purification with a protein from the small ribosomal subunit (40S) in order to have a look at the translated RNAs.

2022-10-01 | GSE160642 | GEO

Translational activators and mitoribosomal isoforms cooperate to mediate mRNA-specific translation in Schizosaccharomyces pombe mitochondria

Project description:Mitochondrial mRNAs encode key subunits of the oxidative phosphorylation complexes that produce energy for the cell. In Saccharomyces cerevisiae, mitochondrial translation is under the control of translational activators, specific to each mRNA. In Schizosaccharomyces pombe, which more closely resembles the human system by its mitochondrial DNA structure and physiology, most translational activators appear to be either lacking, or recruited for post-translational functions. By combining bioinformatics, genetic and biochemical approaches we identified two interacting factors, Cbp7 and Cbp8, controlling Cytb production in S. pombe. We show that their absence affects cytb mRNA stability and decreases the accumulation of the Cytb protein. We further identified two classes of Cbp7/Cbp8 partners and showed that they modulated Cytb or Cox1 synthesis. First, two isoforms of bS1m small mitoribosomal subunits, that appear mutually exclusive and confer translational specificity. Second, a complex of four proteins dedicated to Cox1 synthesis, which includes an RNA helicase that interacts with the mitochondrial ribosome. Our results suggest that S. pombecontains, in addition to complexes of translational activators, a heterogeneous population of mitochondrial ribosomes that could specifically modulate translation depending on the mRNA translated, in order to optimally balance the production of different respiratory complex subunits.

2021-10-11 | PXD025400 | Pride

Frac-seq reveals preferential polyribosome association of minor mRNA isoforms

Project description:The goal of this study was to test the hypothesis that minor alternative mRNA isoforms can be preferentially translated.

2013-06-13 | GSE45237 | GEO

Two functionally distinct human Pan3 isoforms regulate mRNA turnover across the transcriptome

Project description:Human Pan3 protein has two functionally distinct isoforms required for proper decay of mRNA across the transcriptome.

2018-02-14 | GSE86549 | GEO

Frac-seq reveals preferential polyribosome association of minor mRNA isoforms

Project description:The goal of this study was to test the hypothesis that minor alternative mRNA isoforms can be preferentially translated. Included are Cytoplasm and Polyribosome samples in duplicate from both Control and Rapamycin treated cells.

2013-06-13 | E-GEOD-45237 | biostudies-arrayexpress

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