Abstract
BackgroundSm 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.ResultsWe 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.ConclusionsThis 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.
Highlights
Sm proteins are multimeric RNA-binding factors, found in all three domains of life
Identification of RNAs that co-purify with eukaryotic Sm proteins As mentioned above, the Sm and Sm-like proteins comprise a family of ancient evolutionary origin that functions to modulate the stability and translation of several classes of RNA, including mRNAs [1,35]
Trailer Hitch (Tral) is not incorporated into the canonical Sm ring; we expected it to associate with a distinct subset of transcripts [36]
Summary
Eukaryotic Sm proteins, together with their associated RNAs, form small ribonucleoprotein (RNP) complexes important in multiple aspects of gene regulation. Sm proteins are a family of highly conserved RNA-binding proteins present in all three domains of life [1,2]. Sm homologs form either homohexameric (for example, Sm2 and Hfq) or homoheptameric (Sm1) ring-shaped complexes [3,4]. These complexes regulate the stability and translation of mRNAs by facilitating base pairing interactions between small RNAs (sRNAs) and mRNAs [5,6,7]. Canonical Sm proteins form heptamers that bind the major and minor uridine-rich small nuclear
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