Identification of RNAs that can accept assembly of an Sm-protein ring
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ABSTRACT:
PROVIDER: PRJNA1167748 | ENA |
REPOSITORIES: ENA
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Project description:Sm-ring assembly is important for the biogenesis, stability, and function of uridine-rich small nuclear RNAs (U snRNAs) involved in pre-mRNA splicing and histone pre-mRNA 3’ end processing. Assembly of Sm-rings occurs in the cytoplasm and is dependent on a specific sequence and structure motif (Sm-site), ATP, and the Survival motor neuron (SMN) protein complex. The following study informatically investigates the occurence of Sm-sites within the mouse and human transcriptomes and biochemically assesses whether these sites can accept Sm-rings. Sm-sites were found on snRNAs, but are highly prevalent in the 3’ untranslated regions (3’UTR) of long mRNAs. RNA immunoprecipitation experiments confirm that Sm-site containing mRNAs associate with Sm-proteins in the cytoplasm. Established Sm-ring assembly assays were modified to identify polyA-RNAs that specifically associate with Sm-proteins in an ATP-dependent manner, modeling newly assembled Sm-rings. Sm-rings were then specifically assembled onto candidate Sm-site containing mRNAs in an ATP and Sm-site dependent manner. mRNAs containing Sm-sites are down-regulated in models of SMA, suggesting reduced Sm-ring assembly on these mRNAs may contribute to the mechanism of SMA pathogenesis. Together, this study establishes that Sm-site containing mRNAs can accept Sm-rings and identifies a novel mechanism for Sm-proteins in regulation of cytoplasmic mRNAs.
2025-08-27 | GSE278538 | GEO
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
Project description:Competing exonucleases that promote 3’ end maturation or degradation direct quality control of small non-coding RNAs, but how these enzymes distinguish normal from aberrant RNAs is poorly understood. The Pontocerebellar Hypoplasia 7 (PCH7)-associated 3’ exonuclease TOE1 promotes maturation of canonical small nuclear RNAs (snRNAs). Here, we demonstrate that TOE1 achieves specificity towards canonical snRNAs by recognizing Sm complex assembly and cap trimethylation, two features that distinguish snRNAs undergoing correct biogenesis from other small non-coding RNAs. Indeed, disruption of Sm complex assembly via snRNA mutations or protein depletions obstructs snRNA processing by TOE1, and in vitro snRNA processing by TOE1 is stimulated by a trimethylated cap. An unstable snRNA variant that normally fails to undergo maturation becomes fully processed by TOE1 when its degenerate Sm binding motif is converted into a canonical one. Our findings uncover the molecular basis for how TOE1 distinguishes snRNAs from other small non-coding RNAs and explain how TOE1 promotes maturation specifically of canonical snRNAs undergoing proper processing.
2023-09-06 | GSE240773 | GEO
Project description:Competing exonucleases that promote 3’ end maturation or degradation direct quality control of small non-coding RNAs, but how these enzymes distinguish normal from aberrant RNAs is poorly understood. The Pontocerebellar Hypoplasia 7 (PCH7)-associated 3’ exonuclease TOE1 promotes maturation of canonical small nuclear RNAs (snRNAs). Here, we demonstrate that TOE1 achieves specificity towards canonical snRNAs by recognizing Sm complex assembly and cap trimethylation, two features that distinguish snRNAs undergoing correct biogenesis from other small non-coding RNAs. Indeed, disruption of Sm complex assembly via snRNA mutations or protein depletions obstructs snRNA processing by TOE1, and in vitro snRNA processing by TOE1 is stimulated by a trimethylated cap. An unstable snRNA variant that normally fails to undergo maturation becomes fully processed by TOE1 when its degenerate Sm binding motif is converted into a canonical one. Our findings uncover the molecular basis for how TOE1 distinguishes snRNAs from other small non-coding RNAs and explain how TOE1 promotes maturation specifically of canonical snRNAs undergoing proper processing.
2023-09-06 | GSE240772 | GEO
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.
2013-12-01 | GSE35842 | GEO
Project description:JMJ24 is a RING motif containing Jumonji protein, whose E3 ligase activity is essential for communication between histone methylation and DNA methylation.In Arabidopsis JMJ24 is higly expressed in mature pollen. JMJ24 interacted with RDR2 and a single C4HC3 RING motif enabled JMJ24 to mono-ubiquitinate RDR2 for stabilization. RDR2 acted downsteam of JMJ24 for DNA methylation and local silencing. Here we performed tiling-array-based transcriptome profiling using mature pollen collected from WT and jmj24-1 and found that hundreds of loci encoding transposon elements, noncoding RNAs and protein-coding genes are regulated by JMJ24. WT vs. jmj24-1
2011-12-01 | E-GEOD-29708 | biostudies-arrayexpress
Project description:JMJ24 is a RING motif containing Jumonji protein, whose E3 ligase activity is essential for communication between histone methylation and DNA methylation.In Arabidopsis JMJ24 is higly expressed in mature pollen. JMJ24 interacted with RDR2 and a single C4HC3 RING motif enabled JMJ24 to mono-ubiquitinate RDR2 for stabilization. RDR2 acted downsteam of JMJ24 for DNA methylation and local silencing. Here we performed tiling-array-based transcriptome profiling using mature pollen collected from WT and jmj24-1 and found that hundreds of loci encoding transposon elements, noncoding RNAs and protein-coding genes are regulated by JMJ24.
2011-12-01 | GSE29708 | GEO
Project description:Analysis of binding profile of the Polycomb group protein Sce/Ring in Drosophila melanogaster larvae.
2011-04-03 | E-TABM-988 | biostudies-arrayexpress
Project description:PRMT5 is a type II protein arginine methyltransferase with roles in stem cell biology, reprogramming, cancer and neurogenesis. During embryogenesis in the mouse it was hypothesized that PRMT5 functions with the master germline determinant BLIMP1 to promote primordial germ cell (PGC) specification. Using a Blimp1-Cre germline conditional knockout, we discovered that Prmt5 has no major role in murine germline specification, or the first global epigenetic reprogramming event involving depletion of cytosine methylation from DNA and histone H3 lysine 9 dimethylation from chromatin. Instead, we discovered that PRMT5 functions at the conclusion of PGC reprogramming I to promote proliferation, survival and expression of the gonadal germline program as marked by MVH. We show that PRMT5 regulates gene expression by promoting methylation of the Sm spliceosomal proteins, and significantly altering the spliced repertoire of RNAs in mammalian embryonic cells and primordial cells.
2014-12-05 | GSE63800 | GEO
Project description:PRMT5 is a type II protein arginine methyltransferase with roles in stem cell biology, reprogramming, cancer and neurogenesis. During embryogenesis in the mouse it was hypothesized that PRMT5 functions with the master germline determinant BLIMP1 to promote primordial germ cell (PGC) specification. Using a Blimp1-Cre germline conditional knockout, we discovered that Prmt5 has no major role in murine germline specification, or the first global epigenetic reprogramming event involving depletion of cytosine methylation from DNA and histone H3 lysine 9 dimethylation from chromatin. Instead, we discovered that PRMT5 functions at the conclusion of PGC reprogramming I to promote proliferation, survival and expression of the gonadal germline program as marked by MVH. We show that PRMT5 regulates gene expression by promoting methylation of the Sm spliceosomal proteins, and significantly altering the spliced repertoire of RNAs in mammalian embryonic cells and primordial cells. Examination of transcriptional profile of iPHet (Control) vs. iPKO (Prmt5 knock out) 2i Embryonic Stem Cells
2014-12-05 | E-GEOD-63800 | biostudies-arrayexpress