We have cloned, sequenced, and disrupted the gene encoding Ul small nuclear RNA (snRNA) The nuclei of all eucaryotic cells contain a class of low-molecular-weight capped RNA species designated Uclass small nuclear RNAs (snRNAs) (for a review, see reference 12). Five of these (Ul, U2, U4, U5, and U6) are components of small nuclear ribonucleoprotein particles (snRNPs) that participate in the splicing of mRNA precursors (for a review, see reference 44). A primary function of the U snRNPs is to recognize splicing signals in the premRNA. Even before the mechanism of intron removal was understood, binding of Ul to the substrate was proposed on the basis of potential hydrogen bonding between nine nucleotides near the 5' terminus of the snRNA and mammalian 5' splice junctions. Analysis of compensatory base changes in both human (50) and Saccharomyces cerevisiae (budding yeast) cells (37,38, 40) provided direct proof of base pairing between Ul and 5' splice sites at some, but not all, positions tested. The first 10 nucleotides of Ul snRNA from S. cerevisiae and mammals are identical in spite of differences in the 5' splice site consensus sequences, suggesting that they may have function(s) in addition to substrate recognition (12). Yeast Ul is nearly four times as large as human Ul (18, 41), yet it lacks certain structures otherwise universally conserved (17).The protein components of snRNPs include a common core recognized by specific autoimmune sera, as well as a variable number of polypeptides uniquely associated with a particular snRNA (for a review, see reference 21). The recent isolation of cDNA clones for the three Ul snRNPspecific proteins has allowed mapping of their binding sites on the RNA. A variety of in vitro assays demonstrate that the 70K protein (molecular weight of 55,000) interacts specifically with stem-loop I (31, 34, 45), while the A protein binds to stem-loop II (22,30). The C protein also appears to be associated with the 5' portion of Ul (14), but some controversy exists as to its specific binding site on the RNA (30).
* Corresponding author.Signals which direct the synthesis of U snRNAs have been extensively characterized in higher eucaryotes (for a review, see reference 9). On the basis of ao-amanitin sensitivity, U snRNAs are thought to be transcribed by RNA polymerase II, with the exception of U6, which is a pol III transcript. Several features distinguish their synthesis from that of mRNAs, however. Metazoan snRNA promoters lack a canonical TATA sequence; instead, the position of transcription initiation is specified by a conserved motif centered at -50 to -60 (versus -25 to -35 for mRNA TATA boxes). A distal sequence element located between -200 and -250 is similar to, but not interchangeable with, enhancers located upstream from mRNA coding sequences. Perhaps most intriguing is the 3' box located just downstream of the human Ul and U2 genes, which directs formation of the proper 3' end but is bypassed if transcription was initiated at an mRNA rather than an snRNA promoter. Little is kn...