Gemin5-dependent RNA association to polysomes supports selective translation of mRNA subsets
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE200388 | GEO | 2022/08/24
REPOSITORIES: GEO
Similar Datasets
Project description:Gemin5-dependent RNA association to polysomes supports selective translation of mRNA subsets
| PRJNA824426 | ENA
Project description:We show that upregulation of Gemin5 can be detrimental as it modifies the steady state of mRNAs and enhances alternative splicing (AS) events of genes involved in a broad range of cellular processes. RNA-Seq analyses of the mRNA associated with polysomes in cells with high levels of Gemin5 revealed that a significant fraction of the differential AS events was enriched in polysomes.
2024-08-19 | GSE261488 | GEO
Project description:Purpose: mRNA translation into protein is highly regulated, but the role of mRNA isoforms, noncoding RNAs (ncRNAs), and genetic variants has yet to be systematically studied. Using high-throughput sequencing (RNA-seq), we have measured cellular levels of mRNAs and ncRNAs, and their isoforms, in lymphoblast cell lines (LCL) and in polysomal fractions, the latter shown to yield strong correlations of mRNAs with expressed protein levels. Analysis of allelic RNA ratios at heterozygous SNPs served to reveal genetic factors in ribosomal loading. Methods: RNA-seq was performed on cytosolic extracts and polysomal fractions (3 ribosomes or more) from three lymphoblastoid cell lines. As each RNA fraction was amplified (NuGen kit), and relative contributions from various RNA classes differed between cytosol and polysomes, the fraction of any given RNA species loaded onto polysomes was difficult to quantitate. Therefore, we focused on relative recovery of the various RNA classes and rank order of single RNAs compared to total RNA. Results: RNA-seq of coding and non-coding RNAs (including microRNAs) in three LCLs revealed significant differences in polysomal loading of individual RNAs and isoforms, and between RNA classes. Moreover, correlated distribution between protein-coding and non-coding RNAs suggests possible interactions between them. Allele-selective RNA recruitment revealed strong genetic influence on polysomal loading for multiple RNAs. Allelic effects can be attributed to generation of different RNA isoforms before polysomal loading or to differential loading onto polysomes, the latter defining a direct genetic effect on translation. Several variants and genes identified by this approach are also associated with RNA expression and clinical phenotypes in various databases. Conclusions: These results provide a novel approach using complete transcriptome RNA-seq to study polysomal RNA recruitment and regulatory variants affecting protein translation.
2015-06-30 | GSE66135 | GEO
Project description:Here, we report the genome-wide analysis of snRNAs that are bound to Gemin5 upon protein synthesis inhibition. Upon protein synthesis inhibition, the SMN complex that has a crucial role in the biogenesis of snRNPs dissociates into its subunits, leaving Gemin5 alone. The existence of these subunits was confirmed using a proteomics approach. As Gemin5 has been previously reported to be the RNA-binding protein of the SMN complex, we obtained the sequence of all Gemin5 immunoprecipitated snRNAs. We found that snRNAs that were accumulated on Gemin5 contained extra genomic sequences at the 3'-end. We were thus able to identify novel precursors of all the snRNAs that have not been identified previously. This study also provides a detailed method for the characterization of in vivo captured RNPs using a ribo-proteomics approach. Investigation of snRNAs specifically associated with Gemin5 upon protein synthesis inhibition
2010-06-24 | E-GEOD-20751 | biostudies-arrayexpress
Project description:Purpose: mRNA translation into protein is highly regulated, but the role of mRNA isoforms, noncoding RNAs (ncRNAs), and genetic variants has yet to be systematically studied. Using high-throughput sequencing (RNA-seq), we have measured cellular levels of mRNAs and ncRNAs, and their isoforms, in lymphoblast cell lines (LCL) and in polysomal fractions, the latter shown to yield strong correlations of mRNAs with expressed protein levels. Analysis of allelic RNA ratios at heterozygous SNPs served to reveal genetic factors in ribosomal loading. Methods: RNA-seq was performed on cytosolic extracts and polysomal fractions (3 ribosomes or more) from three lymphoblastoid cell lines. As each RNA fraction was amplified (NuGen kit), and relative contributions from various RNA classes differed between cytosol and polysomes, the fraction of any given RNA species loaded onto polysomes was difficult to quantitate. Therefore, we focused on relative recovery of the various RNA classes and rank order of single RNAs compared to total RNA. Results: RNA-seq of coding and non-coding RNAs (including microRNAs) in three LCLs revealed significant differences in polysomal loading of individual RNAs and isoforms, and between RNA classes. Moreover, correlated distribution between protein-coding and non-coding RNAs suggests possible interactions between them. Allele-selective RNA recruitment revealed strong genetic influence on polysomal loading for multiple RNAs. Allelic effects can be attributed to generation of different RNA isoforms before polysomal loading or to differential loading onto polysomes, the latter defining a direct genetic effect on translation. Several variants and genes identified by this approach are also associated with RNA expression and clinical phenotypes in various databases. Conclusions: These results provide a novel approach using complete transcriptome RNA-seq to study polysomal RNA recruitment and regulatory variants affecting protein translation. cells from 3 samples were grown to 5x105 cells/mL density in T75 tissue culture flask and harvested, total RNA and polysome bound RNA was sequenced by Ion Proton
2015-06-30 | E-GEOD-66135 | biostudies-arrayexpress
Project description:We report the CLIP-seq data of the non-canonical RNA-binding site of Gemin5. This region consists of two domains, RBS1 and RBS2, differing in their RNA-interaction features. Interestingly, the most abundant RNA target of the RBS1 polypeptide was the Gemin5 mRNA. Biochemical and functional characterization of this target demonstrated that RBS1 domain physically interacts with a stem-loop upregulating mRNA translation by counteracting the negative effect of Gemin5 protein on global protein synthesis. We propose that the RBS1 domain of Gemin5 performs a dual role on translation control, which depends on the target RNA, allowing fine-tune the availability of Gemin5 to play its multiple roles in gene expression control
2018-08-30 | GSE102268 | GEO
Project description:Selective translation allows to orchestrate the expression of specific proteins in response to different signals through the concerted action of cis-acting elements and RNA-binding proteins (RBPs). Gemin5 is a ubiquitous RBP involved in snRNP assembly. In addition, Gemin5 regulates translation of different mRNAs through apparently opposite mechanisms of action. Here, we investigated the differential function of Gemin5 in translation by identifying at a genome-wide scale the mRNAs associated with polysomes. Among the mRNAs showing Gemin5-dependent enrichment in polysomal fractions, we identified a selective enhancement of specific transcripts. Comparison of the targets previously identified by CLIP methodologies with the polysome-associated transcripts revealed that only a fraction of the targets was enriched in polysomes. Two different subsets of these mRNAs carry unique cis-acting regulatory elements, the 5' terminal oligopyrimidine tracts (5'TOP) and the histone stem-loop (hSL) structure at the 3' end, respectively, encoding ribosomal proteins and histones. RNA-immunoprecipitation (RIP) showed that ribosomal and histone mRNAs coprecipitate with Gemin5. Furthermore, disruption of the TOP motif impaired Gemin5-RNA interaction, and functional analysis showed that Gemin5 stimulates translation of mRNA reporters bearing an intact TOP motif. Likewise, Gemin5 enhanced hSL-dependent mRNA translation. Thus, Gemin5 promotes polysome association of only a subset of its targets, and as a consequence, it favors translation of the ribosomal and the histone mRNAs. Together, the results presented here unveil Gemin5 as a novel translation regulator of mRNA subsets encoding proteins involved in fundamental cellular processes.
| S-EPMC9392717 | biostudies-literature
Project description:GEMIN5 is a critical component of snRNP assembly complex. Patients carrying novel autosomal recessive variants in the GEMIN5 gene showed symptoms of developmental delay, central hypotonia, and cerebellar ataxia which are distinct than classical spinal muscular atrophy. We performed RNA-seq analysis in iPSC-derived differentiated neurons with biallelic GEMIN5-H913R mutation to identify global alterations in various genes and pathways mediated by GEMIN5 mutations in patients.
2021-03-11 | GSE168622 | GEO
Project description:Here, we report the genome-wide analysis of snRNAs that are bound to Gemin5 upon protein synthesis inhibition. Upon protein synthesis inhibition, the SMN complex that has a crucial role in the biogenesis of snRNPs dissociates into its subunits, leaving Gemin5 alone. The existence of these subunits was confirmed using a proteomics approach. As Gemin5 has been previously reported to be the RNA-binding protein of the SMN complex, we obtained the sequence of all Gemin5 immunoprecipitated snRNAs. We found that snRNAs that were accumulated on Gemin5 contained extra genomic sequences at the 3'-end. We were thus able to identify novel precursors of all the snRNAs that have not been identified previously. This study also provides a detailed method for the characterization of in vivo captured RNPs using a ribo-proteomics approach.
2010-06-24 | GSE20751 | GEO
Project description:To characterize RNA distribution on total and polysomal fractions of hepatocytes, we have employed whole genome microarray expression profiling as a discovery platform to identify differentially abundant mRNAs on polysomes.
2015-10-01 | GSE61126 | GEO