Ontology highlight
ABSTRACT:
PROVIDER: PRJNA834902 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR19085875.fastq.gz | Fastqsanger.gz |
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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: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.
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Project description:Flustrellidra corniculata Raw sequence reads
| PRJNA531442 | ENA