Identification and analysis of RNAs associated with Sm proteins. Zhipeng Lu, Greg Matera. Biology, UNC at Chapel Hill, Chapel Hill, NC., NORTH CAROLINA.

   Sm proteins are a family of highly conserved RNA-binding proteins present in all three domains of life. In eukaryotes, Sm proteins bind small nuclear RNAs (snRNAs) to form snRNPs, which are basic components of the pre-mRNA splicing machinery. However, little is known about other functions of Sm proteins in eukaryotic cells, given their divergent roles in regulating mRNA stability in bacteria and archaea. Our lab recently found that Sm proteins form a complex with oskar mRNA and are required to help specify the germline in Drosophila ovaries. This discovery led us to hypothesize that Sm proteins play important, but so far unrecognized, roles in RNA metabolism and fundamental cellular processes in eukaryotes. To test this hypothesis, we developed a strategy to identify Sm-associated RNAs by deep sequencing immunopurified complexes (RIP-seq). Using this approach, we discovered a subset of mRNAs and novel unannotated non-coding RNAs that associate with Sm proteins. The association between mRNAs and Sm proteins is independent of splicing. Many of the Sm-associated mRNAs encode mitochondrial and ribosomal proteins. Furthermore a number of these mRNAs colocalize with Sm proteins in the oocyte cortex, a region rich in mitochondria. Together with our previous results, these findings support the view that Sm proteins function in mRNA transport and/or localized translation. In addition to novel Sm-bound mRNA targets, one of the non-coding RNAs we identified is encoded by a newly-evolved snRNA gene. This young gene is present only within a subset of Drosophilids. We identified a putative base-pairing region with U6 snRNA, suggesting a role for this novel snRNA in splicing regulation.