C/D box snoRNAs involved in ribose methylation contain one or two long 10-21 bp stretches of exact complementarity to ribosomal RNA, and four conserved box features: C, C', D and D' boxes (see Figure 1.1). The C and D box sequence motifs are required for snoRNA nucleolar localization, accumulation, and association with the ribonucleoprotein particle complexes (RNPs). The C' and D' boxes are necessary for methylation guide function [Kiss-Laszlo et al., 1998]. The position of 2'-O-methylation of rRNA is within the helix formed by the complementary guide sequence of the snoRNA, and precisely 5 nt upstream of box D or D'.
Genetic disruption of the U24 snoRNA in S. cerevisiae causes loss of the predicted target methyl groups [Kiss-Laszlo et al., 1996]. The same study showed that alteration of the rRNA complementary region was sufficient to cause addition of a predictable ectopic methyl at a new position on the rRNA. snoRNA depletion experiments in Xenopus oocytes have showed that methylation guide snoRNAs are necessary for specific methylation in vertebrates as well [Tycowski et al., 1996,Dunbar & Baserga, 1998]. Methylation guide snoRNAs may also modify other RNAs, including the U6 spliceosomal RNA [Tycowski et al., 1998]. A particularly intriguing experiment showed guide snoRNAs could be engineered to modify mRNA by inserting an appropriate complementary region, albeit at low efficiency [Cavaille et al., 1996].
Interestingly, one essential yeast snoRNA, U14, functions in both cleavage and ribose rRNA modification [Jarmolowski et al., 1990], using two different rRNA complementarities (one for cleavage, one for guiding methylation). snR10, an H/ACA box snoRNA, is also a dual function snoRNA, involved in cleavage and pseudouridylation. Surprisingly, all others snoRNAs involved in rRNA modification are non-essential, implying the modifications they specify are not essential. So, just what are all these modifications for? Despite over 30 years of research into rRNA modifications, this question still has no definitive answer.