next up previous contents
Next: Genomic Organization of the Up: Discussion Previous: Multiple Methylations Guided by

Methylation Guide snoRNA Consensus Structure

With a large number of the 2'-O-methylation guide snoRNAs identified and confirmed in S. cerevisiae, we now have an improved consensus structure for this gene family. The structure is similar to that presented by Kiss-Laszlo et al. (1996), now with more clearly defined lengths between features. Some aspects of the expanded sample of snoRNA features are worth noting. Two snoRNAs break with the canonical ``CUGA'' D box sequence. There is a fairly tight length distribution between features, which we used to our advantage to eliminate false positives. For the D' box guided sites, the complementary sequence always occurs within 25 bp of the C box, and the gap between the D' and D boxes (3' end) is always two or more times longer than the gap between the C box and complementary sequence (5' end). Thus, the complementary sequence never occurs directly in the middle of snoRNAs. We also noted a strong bias towards uridine at the nucleotide immediately 5' to the guide D or D' box (U 61%, A 26%, G 9%, C 4%). This may be a valid extension of the D/D' box motif. Examination of the snoRNA-rRNA duplex matches/mismatches (Table 4.2) shows that 17 duplexes contain at least one G-U pairing. Almost as many duplexes contain non-Watson-Crick, non-G-U pairs as well, violating the commonly described ``perfect'' stretches of snoRNA/rRNA pairing. Also, no clear patterns emerged for snoRNAs containing terminal stem loops. All intronic snoRNAs had at least weak terminal stems, although roughly half of the extragenic and tandem array snoRNAs also contained stems. Double guide snoRNAs also do not show a consistent pattern for stem formation.


next up previous contents
Next: Genomic Organization of the Up: Discussion Previous: Multiple Methylations Guided by
Todd M. Lowe
2000-03-31