Similar Datasets
Project description:Mapping 3'ends of cleaved mRNAs derived from a reporter that is subject to no-go decay for the purpose of characterizing the cleavage reaction.
2017-08-01 | GSE101667 | GEO
Project description:RPS3, a universal core component of the 40S ribosomal subunit, interacts with mRNA at the entry channel. Whether RPS3 mRNA-binding contributes to specific mRNA translation and ribosome specialization in mammalian cells is unknown. Here we mutated RPS3 mRNA-contacting residues R116, R146 and K148 and report their impact on cellular and viral translation. R116D weakened cap-proximal initiation and promoted leaky scanning, while R146D had the opposite effect. Additionally, R146D and K148D displayed contrasting effects on start-codon fidelity. Translatome analysis uncovered common differentially translated genes of which the downregulated set bears long 5’UTR and weak AUG context, suggesting a stabilizing role during scanning and AUG selection. We identified an RPS3-dependent regulatory sequence (RPS3RS) in the sub-genomic 5’UTR of SARS-CoV-2 consisting of a CUG initiation codon and a downstream element that is also the viral transcription regulatory sequence (TRS). Furthermore, RPS3 mRNA-binding residues were essential for SARS-CoV-2 NSP1-mediated inhibition of host translation and for its ribosomal binding. Intriguingly, NSP1-induced mRNA degradation was also reduced in R116D cells, indicating that mRNA decay occurs in the ribosome context. Thus, RPS3 mRNA-binding residues have multiple translation regulatory functions and are exploited by SARS-CoV-2 in various ways to influence host and viral mRNA translation and stability.
2023-04-12 | GSE217181 | GEO
Project description:The human ribosomal protein S3 (RPS3), a component of the small 40S ribosomal subunit, is mainly involved in ribosomal maturation and initiation of translation through association with initiation factors. In this study, we firstly identified that RPS3 played an important role in HCC progression. We performed RNA sequencing to profile gene expression patterns before and after RPS3 knockdown.
2019-02-01 | GSE118140 | GEO
Project description:Angiotensin II (Ang II) treatment contributes to hypertrophic growth and mitochondrial dysfunction in hiPSC-derived cardiomyocytes. Here, we report enhanced RPS3 phosphorylation at serine 149 in nuclear compartment and abnormal mitochondrial biogenesis during Ang II incubation. Furthermore, RPS3 S149 mutation attenuated Ang II induced cardiomyocyte hypertrophy and improved mitochondrial biogenesis and dysfunction. Mechanistically, RPS3 Ser149 mutation promoted mitochondrial RNA stabilization and blunt Ang II induced mitochodnrial RNA alternative splicing for degradation, by which RPS3 dephosphorylation restored mitochondrial complex assembly in cardiomyocytes.
2023-07-30 | GSE238123 | GEO
Project description:Translation of poly(A) tails leads to mRNA cleavage but the mechanism and global pervasiveness of this “nonstop/no-go” decay process is not understood. Here we performed ribosome profiling of short 15-18 nt mRNA footprints to identify ribosomes stalled at 3’ ends of mRNA decay intermediates. We found mRNA cleavage extending hundreds of nucleotides upstream of ribosome stalling in poly(A) and predominantly in one reading frame. These observations suggest that cleavage is closely associated with the ribosome. Surprisingly, ribosomes appeared to stall when as few as 3 consecutive ORF-internal lysine codons were positioned in the A, P, and E sites though significant mRNA degradation was not observed. Endonucleolytic cleavage was widespread, however, at sites of premature polyadenylation and rescue of the ribosomes stalled at these sites was dependent on Dom34. These results suggest this process may be critical when changes in polyadenylation occur during development, tumorigenesis, or when translation termination/recycling is impaired.
2017-01-22 | GSE85944 | GEO
Project description:Drosophila melanogaster RpS3, Ribosomal protein S3, is differentially expressed in 5 experiment(s);
| FBgn0002622 | ExpressionAtlas
Project description:Drosophila melanogaster RpS3, Ribosomal protein S3, is expressed in 4 baseline experiment(s);
| FBgn0002622 | ExpressionAtlas
Project description:Bacteria depend on efficient RNA turnover to rapidly alter gene expression, essentially for responding to changing conditions. Nevertheless, remarkably few details are known about the rate-limiting steps in targeting and decay of RNA. The membrane-anchored endoribonuclease RNase Y is a virulence factor in Gram- positive pathogens. We have obtained a global picture of RNase Y sequence specificity using RNA-seq and the novel transcriptome-wide EMOTE method. Ninety- nine endoribonucleolytic sites produced in vivo were precisely mapped, notably inside six out of seven genes whose half-lives increase the most in an RNase Y deletion mutant, and additionally to three separate transcripts encoding degradation ribonucleases, including RNase Y itself, suggesting a regulatory network. We show that RNase Y is required to initiate the major degradation pathway of a defined sub-set of transcripts that are inaccessible to other ribonucleases, but is prevented from promiscuous activity by membrane confinement and sequence preference for guanosines. Rnase Y activity in S. aureus is analysed on a genome wide scale under two perspectives: a RNA decay timecourse with mRNA-seq; and exact position of cleavage with an EMOTE assay (Exact Mapping Of Trancripts Ends)
2015-09-01 | E-GEOD-68811 | biostudies-arrayexpress
Project description:Rattus norvegicus Rps3, ribosomal protein S3 [Source:RGD Symbol;Acc:619888], is expressed in 6 baseline experiment(s);
| ENSRNOG00000017418 | ExpressionAtlas