In summing all expressed snoRNAs that have either been verified or strongly predicted to guide ribose methylation, we count 41 genes that can be assigned to 51 rRNA methylation sites (Table 4.2). We estimate that up to two methylation guide snoRNAs remain to be identified for the two unassigned methylation sites (SSU-Am436, SSU-Gm?), and two to four snoRNAs may be identified as being redundant with known snoRNAs for SSU-Um1265, SSU-Cm1637, LSU-Um2918, and LSU-Gm2919.
In addition to the 22 new guide snoRNAs we identified and verified (Table 4.2, snoRNAs in boldface), we were able to verify that a number previously identified C/D box snoRNAs guide methylation at additional methyl sites. The search program pointed out that snR40, snR41, snR47, and snR48 each contain additional methylation target sites, each of which we were able to verify experimentally. The program was also able to classify snR13, a previously known C/D box snoRNA for which the function was undetermined [Smith et al., 1997].
Eight previously identified C/D box snoRNAs that we predicted as methylation guide snoRNAs and verified experimentally appear in Genbank as the ``Z'' snoRNAs (SCSNORZ2 - SCSNORZ8, SCZ9SNOR; Zhou, H. and Qu, L.H., unpublished). It was recently suggested but not experimentally shown that these are legitimate guide snoRNAs [Cavaille & Bachellerie, 1998]. With demonstration of function, we suggest assigning the standard ``snR'' names snR72 through snR79 to Z2 through Z9. While this manuscript was in preparation, seven additional Z snoRNAs were deposited in Genbank as Z10-Z16 (Zhou, H. and Qu, L.H.), again with no reference to function or scientific publication. All seven correspond to snoRNAs independently identified, assigned to methylation sites, and verified as novel snoRNAs in this work (Table 4.2), and we propose snR names for them as well.
Some snoRNAs may direct other modifications not detected by the dNTP concentration-dependent primer extension assay, or may have other functions in assembly of the ribosome. Currently, only three identified C/D box snoRNAs have no demonstrated function: snR4, and snR45, and snR190. All three have been shown to be nonessential [Zagorski et al., 1988,Balakin et al., 1996]. Our search program did not detect any rRNA complementarities in snR4 or snR45, thus we cannot predict their function. For snR190, our program agrees with a possible target modification site previously suggested by Kiss-Laszlo et al. (1996). However, based on experimental evidence, we believe such a ribose methyl site does not exist or is too weakly methylated to be detected by our rRNA methyl mapping experiments.