Autoimmune sera of the Sm specificity react with the major class of small nuclear RNA (snRNA)-containing ribonucleoprotein particles (snRNP's) from organisms as evolutionarily divergent as insects and dinoflagellates but have been reported not to recognize snRNP's from yeast. The Sm antigen is thought to bind to a conserved snRNA motif that includes the sequence A(U3-6)G. The hypothesis was tested that yeast also contains functional analogues of Sm snRNA's, but that the Sm binding site in the RNA is more strictly conserved than the Sm antigenic determinant. After microinjection of labeled yeast snRNA's into Xenopus eggs or oocytes, two snRNA's from Saccharomyces cerevisiae become strongly immunoprecipitable with human auto-antibodies known as anti-Sm. These each contain the sequence A(U5-6)G, are essential for viability, and are constituents of the spliceosome. At least six other yeast snRNA's do not become immunoprecipitable and lack this sequence; these non-Sm snRNA's are all dispensable.

Previous work showed that the simple eukaryote Saccharomyces cerevisiae contains a group of RNAs with the general structural properties predicted for small nuclear RNAs (snRNAs), including possession of the characteristic trimethylguanosine 5'-terminal cap. It was also demonstrated that, unlike their metazoan counterparts, the yeast snRNAs are present in low abundance (200-500 molecules per haploid cell). We have now used antibody directed against the 5' cap to investigate the total set size of snRNAs in this organism. We present evidence that the number of distinct yeast snRNAs is on the order of several dozen, that the length of the capped RNAs can exceed 1000 nucleotides, and that the relative abundance of a subset of these RNAs is 1/5th to 1/20th that ofthe class ofsnRNAs described previously. These findings suggest that the six highly abundant species of snRNAs (Ul-U6) typically reported in metazoans may represent a serious underestimation of the total diversity of snRNAs in eukaryotes.Studies of small nuclear RNAs (snRNAs) have focused on the six so-called U-RNAs (U1-U6), first discovered some 15 years ago (for review, see ref. 1). In metazoans, these RNAs range in length from 90 to 216 nucleotides (nt), are extremely abundant (there are =106 U1 molecules in a HeLa cell, for example) and are encoded by multigene families (2, 3). Although functional studies have lagged behind structural characterization, these RNAs are widely believed to mediate a spectrum of RNA-processing reactions in eukaryotic cells. Indeed, recent information from in vitro analyses directly implicates the involvement of U1 (4-6), U2 (7,8), and probably U5 (9) in pre-mRNA splicing. Similarly, one or more U-RNAs appear to be required for 3' end formation/ polyadenylylation in vitro (10, 11), although the specific suggestion that these are U4/U6 (12) has not been verified. Finally, the involvement of U3 in rRNA maturation is deemed likely because U3 is restricted to the nucleolus and appears to be hydrogen-bonded to 14).Several years ago, we initiated a search for snRNAs in the simple eukaryote Saccharomyces cerevisiae, with the goal of exploiting the powerful genetic tools available in this organism. As described (15, 16), a group of RNAs were identified that conformed to several predicted criteria. These included small size, nuclear localization, metabolic stability, and possession of the characteristic trimethylguanosine 5' cap. The latter characteristic provides a particularly powerful diagnostic in that snRNAs are the only class of RNAs known to possess this terminus. However, it was also shown that the yeast snRNAs differ in several potentially important ways from U1-U6. A significant asset to our genetic strategy was the finding (15,17,18) that the six yeast RNAs tested (designated snR3, snR4, snR7, snR8, snR9, and snR10) are encoded by single-copy genes (designated SNR3, etc.). In keeping with this lack ofgenetic redundancy, the yeast RNAs are present in low abundance: 200-500 molecules per haploid cell (15).A further surp...