Small nucleolar RNAs (snoRNAs) are involved in precursor ribosomal
RNA (pre-rRNA) processing and rRNA base modification
(2′-O-ribose methylation and pseudouridylation).
In all eukaryotes, certain snoRNAs (e.g., U3) are
transcribed from classical promoters. In vertebrates, the majority
are encoded in introns of protein-coding genes, and are released
by exonucleolytic cleavage of linearized intron lariats. In
contrast, in maize and yeast, nonintronic snoRNA gene clusters
are transcribed as polycistronic pre-snoRNA transcripts from
which individual snoRNAs are processed. In this article, 43
clusters of snoRNA genes, an intronic snoRNA, and 10 single
genes have been identified by cloning and by computer searches,
giving a total of 136 snoRNA gene copies of 71 different snoRNA
genes. Of these, 31 represent snoRNA genes novel to plants.
A cluster of four U14 snoRNA genes and two clusters
containing five different snoRNA genes (U31,
snoR4, U33, U51, and snoR5)
from Arabidopsis have been isolated and characterized.
Of these genes, snoR4 is a novel box C/D snoRNA that
has the potential to base pair with the 3′ end of 5.8S
rRNA and snoR5 is a box H/ACA snoRNA gene. In addition,
42 putative sites of 2′-O-ribose methylation
in plant 5.8S, 18S, and 25S rRNAs have been mapped by primer
extension analysis, including eight sites novel to plant rRNAs.
The results clearly show that, in plants, the most common gene
organization is polycistronic and that over a third of predicted
and mapped methylation sites are novel to plant rRNAs. The
variation in this organization among gene clusters highlights
mechanisms of snoRNA evolution.