A nomenclature is described for restriction endonucleases, DNA methyltransferases, homing endonucleases and related genes and gene products. It provides explicit categories for the many different Type II enzymes now identified and provides a system for naming the putative genes found by sequence analysis of microbial genomes.

Cajal (coiled) bodies are conserved subnuclear organelles that are present in the nucleoplasm of both animal and plant cells. Although Cajal bodies were ®rst described nearly 100 years ago, their function has remained largely speculative. Here, we describe a novel class of human small nuclear RNAs that localize speci®cally to Cajal bodies. The small Cajal bodyspeci®c RNAs (scaRNAs) are predicted or have already been demonstrated to function as guide RNAs in site-speci®c synthesis of 2¢-O-ribose-methylated nucleotides and pseudouridines in the RNA polymerase II-transcribed U1, U2, U4 and U5 spliceosomal small nuclear RNAs (snRNAs). Our results provide strong support for the idea that the Cajal body, this mysterious nuclear organelle, provides the cellular locale for post-transcriptional modi®cation of spliceosomal snRNAs.

Pseudouridine, the most abundant modified nucleoside in RNA, is synthesized by posttranscriptional isomerization of uridines. In eukaryotic RNAs, site-specific synthesis of pseudouridines is directed primarily by box H/ACA guide RNAs. In this study, we have identified 61 novel putative pseudouridylation guide RNAs by construction and characterization of a cDNA library of human box H/ACA RNAs. The majority of the new box H/ACA RNAs are predicted to direct pseudouridine synthesis in rRNAs and spliceosomal small nuclear RNAs. We can attribute RNA-directed modification to 79 of the 97 pseudouridylation sites present in the human 18S, 5.8S, and 28S rRNAs and to 11 of the 21 pseudouridines reported for the U1, U2, U4, U5, and U6 spliceosomal RNAs. We have also identified 12 novel box H/ACA RNAs which lack apparent target pseudouridines in rRNAs and small nuclear RNAs. These putative guide RNAs likely function in the pseudouridylation of some other types of cellular RNAs, suggesting that RNA-guided pseudouridylation is more general than assumed before. The genomic organization of the new box H/ACA RNA genes indicates that in human cells, all box H/ACA pseudouridylation guide RNAs are processed from introns of pre-mRNA transcripts which either encode a protein product or lack protein-coding capacity.Posttranscriptional covalent modification of ribonucleotides is an important step in the biosynthesis of stable cellular RNAs, including tRNAs, rRNAs, small nuclear RNAs (snRNAs), and small nucleolar RNAs (snoRNAs) (40). Biochemical, biophysical, and genetic studies have shown that modified nucleotides are important for the appropriate function of mature RNAs; they facilitate correct RNA folding and contribute to the formation of appropriate RNA-RNA and RNA-protein interactions (reviewed in references 1, 7, 12, 15, and 44).While in tRNAs, most modified nucleotides are synthesized by protein enzymes, in eukaryotic rRNAs and snRNAs, sitespecific synthesis of the most prevalent modified ribonucleotides, the 2Ј-O-ribose-methylated nucleotides and the pseudouridines, is achieved by two distinct families of ribonucleoproteins (RNPs) (reviewed in references 14, 18, 27, 28, and 52). The modification guide RNPs consist of a sequence-specific guide RNA and a set of common proteins. Each 2Ј-O-ribose methylation guide RNA carries the conserved C, CЈ (consensus, RUGAUGA), D, and DЈ (CUGA) box motifs and possesses one or two 10-to 21-nucleotide-long antisense elements that are responsible for selection of the correct substrate ribonucleotides through the formation of double helices with the target RNAs (11, 32). The selected ribonucleotides are 2Ј-O-ribose methylated by the Nop1p/fibrillarin methyltransferase enzyme that, in addition to the Snu13 (15.5-kDa), Nop56p, and Nop58p RNP proteins, is associated with all box C/D RNAs (14, 18, 27, 52, 55).The pseudouridylation guide RNAs are composed of two major hairpin elements that are connected by a hinge and followed by a short tail region (Fig. 1A). The single-stranded hinge and tail region ...