Identification of a Novel Element Required for Processing of Intron-Encoded Box C/D Small Nucleolar RNAs in Saccharomyces cerevisiae

Abstract

Processing of intron-encoded box C/D small nucleolar RNAs (snoRNAs) in metazoans through both the splicing-dependent and -independent pathways requires the conserved core motif formed by boxes C and D and the adjoining 5′-3′-terminal stem. By comparative analysis, we found that five out of six intron-encoded box C/D snoRNAs in yeast do not possess a canonical terminal stem. Instead, complementary regions within the flanking host intron sequences have been identified in all these cases. Here we show that these sequences are essential for processing of U18 and snR38 snoRNAs and that they compensate for the lack of a canonical terminal stem. We also show that the Rnt1p endonuclease, previously shown to be required for the processing of many snoRNAs encoded by monocistronic or polycistronic transcriptional units, is not required for U18 processing. Our results suggest a role of the complementary sequences in the early recognition of intronic snoRNA substrates and point out the importance of base pairing in favoring the communication between boxes C and D at the level of pre-snoRNA molecules for efficient assembly with snoRNP-specific factors.

ACKNOWLEDGMENTS

We thank Manny Ares for the generous gift of the RNT1and rnt1-Δ strains. We thank members of our laboratory, in particular, Alessandro Fatica and Corinna Giorgi, for many helpful discussions. We thank Ida Ruberti and Giorgio Morelli for suggestions on sequence analysis. We also thank Massimo Arceci and Genesio Ricci for technical help.

T.V. was the recipient of an Istituto Pasteur-Fondazione Cenci Bolognetti fellowship. F.C. was the recipient of a fellowship from Fondazione Adriano Buzzati-Traverso. This work was partially supported by grants from MURST-CNR Biotechnology Program L.95/95 from PRIN 40% of MURST and from CNR Target Project on Biotechnology.