With nearly all methylation guide snoRNAs identified, we can assess the general genomic organization of the gene family (Table 4.2). All chromosomes except VI contain at least one methylation guide snoRNA. Most are dispersed as independent singlets or within five small clusters of 2-7 tandemly arrayed guide snoRNAs. A total of 19 singlets occur outside of known protein coding genes, presumably as independent transcription units. All tandemly arrayed snoRNAs within the same cluster are oriented on the same strand, and are separated by between 80 to 148 bp. Recent results indicate these genes are polycistronic [Petfalski et al., 1998,Chanfreau et al., 1998a,Chanfreau et al., 1998b,Qu et al., 1999]. Six yeast snoRNAs occur within the introns of host protein genes, all on the pre-mRNA coding strand. The mixture of snoRNAs in yeast occurring within introns, tandem arrays, and as singlets is in contrast to vertebrates, where all currently known guide snoRNAs are within host gene introns. Polycistronic arrays of snoRNAs have also been reported in plants [Leader et al., 1997,Shaw et al., 1998]. Some plant polycistrons contain a mix of snoRNAs from both major families of guide snoRNAs (C/D box and H/ACA box snoRNAs), whereas none of the yeast tandem arrays contain members outside of the C/D box family.
It has long been noted that C/D box snoRNAs often occur in the introns of ribosomal proteins in vertebrates [Maxwell & Fournier, 1995]. Only two C/D box snoRNAs, snR39 and snR59, occur in ribosomal proteins of yeast, but an unexpectedly large number, ten, occur immediately adjacent to ribosomal proteins. These snoRNAs occur more often on the opposite strand than the same strand as the ribosomal protein genes.