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Genome-wide analysis of snRNAs bound to Gemin5 upon protein synthesis inhibition

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE20751 | GEO | 2010/06/24

SECONDARY ACCESSION(S): PRJNA124999

REPOSITORIES: GEO

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Genome-wide analysis of snRNAs bound to Gemin5 upon protein synthesis inhibition

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

RNA maps of the non-canonical RNA-binding site of Gemin5

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

Mutations in GEMIN5 cause a neurodevelopmental ataxia syndrome by a loss-of-1function mechanism

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

Homo sapiens

Project description:Genome-wide analysis of snRNAs bound to Gemin5 upon protein synthesis inhibition

| PRJNA124999 | ENA

Gemin5-dependent RNA association to polysomes supports selective translation of mRNA subsets

Project description:Here we report the identification at a genome-wide scale of the mRNAs associated to polysomes in Gemin5-depleted cells relative to control cells. Among the polysomal Gemin5-enhanced mRNAs, we identified numerous transcripts belonging to two distinct families, which encode ribosomal proteins and histones.

2022-08-24 | GSE200388 | GEO

Alternative splicing events driven by altered levels of Gemin5 undergo translation

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

Human HEK293 Gemin5 clinical variants LC-MSMS

Project description:Identification of cellular proteins interacting with Gemin5 variants found in patients with neurological disorders. P85 C-terminal fragment of Gemin5 has been used to purify the protein complexes associated by Tandem Affinity Purification. The study has been performed using two biological replicates of each bait protein: p85-WT, the dimerization mutant p85-A951E, and the clinical variants p85-R1016C, p85-D1019E and p85-L1367P.

2022-04-06 | PXD028959 | Pride

RIP-seq analysis of eukaryotic Sm proteins identifies three major categories of Sm-containing ribonucleoproteins

Project description:Background: Sm proteins are multimeric RNA-binding factors, found in all three domains of life. Eukaryotic Sm proteins, together with their associated RNAs, form small ribonucleoprotein (RNP) complexes important in multiple aspects of gene regulation. Comprehensive knowledge of the RNA components of Sm RNPs is critical for understanding their functions. Results: We developed a multi-targeting RNA-immunoprecipitation sequencing (RIP-seq) strategy to reliably identify Sm-associated RNAs from Drosophila ovaries and cultured human cells. Using this method, we discovered three major categories of Sm-associated transcripts: small nuclear (sn)RNAs, small Cajal body (sca)RNAs and mRNAs. Additional RIP-PCR analysis showed both ubiquitous and tissue-specific interactions. We provide evidence that the mRNA-Sm interactions are mediated by snRNPs, and that one of the mechanisms of interaction is via base pairing. Moreover, the Sm-associated mRNAs are mature, indicating a splicing-independent function for Sm RNPs. Conclusions: This study represents the first comprehensive analysis of eukaryotic Sm-containing RNPs, and provides a basis for additional functional analyses of Sm proteins and their associated snRNPs outside of the context of pre-mRNA splicing. Our findings expand the repertoire of eukaryotic Sm-containing RNPs and suggest new functions for snRNPs in mRNA metabolism. RNA-Immunoprecipitation sequencing of RNA-Sm protein complexes.

2013-12-01 | E-GEOD-35842 | biostudies-arrayexpress

Identification of Survival Motor Neuron (SMN) complexes in Drosophila using affinity purification-mass spectrometry analysis

Project description:Molecular chaperones and co-chaperones are highly conserved cellular components that perform variety of duties related to the proper three-dimensional folding of the proteome. The Survival Motor Neuron (SMN) complex is an RNP assembly chaperone and serves as a paradigm for studying how specific small nuclear (sn)RNAs are identified and paired with their client substrate proteins. SMN forms the oligomeric core of this complex, and missense mutations in its YG box self-interaction domain are known to cause Spinal Muscular Atrophy (SMA). The basic framework for understanding how snRNAs are assembled into U-snRNPs is known, the pathways and mechanisms used by cells to regulate their biogenesis are poorly understood. Given the importance of these processes to normal development as well as neurodegenerative disease, we set out to identify and characterize novel SMN binding partners. Here, we carried out affinity purification mass spectrometry (AP-MS) of SMN using stable fly lines exclusively expressing either wildtype or SMA-causing missense alleles. Bioinformatic analyses of the pulldown data, along with comparisons to proximity labeling studies carried out in human cells, revealed conserved connections to at least two other major chaperone systems including heat shock folding chaperones (HSPs) and histone/nucleosome assembly chaperones.

2024-09-11 | PXD053506 | Pride

Differential pre-mRNA defects in fission yeast carrying a temperature degron allele of the SMN gene

Project description:The SMA disease results from deletions or mutations in the “survival of motor neuron” (SMN1) gene. The SMN protein plays an essential role in the biogenesis of spliceosomal snRNPs but the link between a defect in this process and specific splicing inhibition is not known. Here, we report the construction of a temperature degron (td) allele of the S. pombe SMN protein and show that its depletion at 37°C affects snRNPs stability and splicing. In addition, the function of the tdSMN allele in snRNPs assembly is affected already at 25°C suggesting a deleterious effect of the tag at this temperature. Remarkably, using S. pombe tiling arrays and RT-PCR validation tests, we report that splicing is altered differentially in the tdSMN cells at permissive temperature. Our results suggest that the defects observed in tdSMN fission yeast cells mimic splicing deficits observed in SMN-deficient metazoan cells.

2010-04-22 | GSE17010 | GEO

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