snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs

Abstract

The snoRNA-LBME-db is a dedicated database containing human C/D box and H/ACA box small nucleolar RNAs (snoRNAs), and small Cajal body-specific RNAs (scaRNAs). C/D box and H/ACA box snoRNAs are part of ribonucleoparticles that guide 2'-O-ribose methylation and pseudouridilation, respectively, of selected residues of 28S, 18S or 5.8S rRNAs or of the spliceosomal U6 RNA. Similarly, scaRNAs guide modifications of the spliceosomal RNAs transcribed by RNA polymerase II (U1, U2, U4, U5 and U12) and are often composed of both C/D box and H/ACA box domains. However, some snoRNAs do not function as modification guide RNAs, but rather as RNA chaperones during the maturation of pre-rRNA. The database was built by a compilation of the literature, and comprises human sno/scaRNAs that were experimentally verified, as well as the human orthologs of snoRNAs that were cloned in other vertebrate species, and some snoRNAs that are predicted by bioinformatics search in loci submitted to genomic imprinting, but have not all been experimentally verified. For each entry, the database identifies the modified nucleotide(s) in the target RNA(s), indicates the corresponding predicted base pairing, gives a few pertinent references and provides a link to the position of the sno/scaRNA on the UCSC Genome Browser. The 'Find guide RNA' function allows one to find the sno/scaRNAs predicted to guide the modification of a particular nucleotide in the rRNA and spliceosomal RNA sequences. The 'Browse' function allows one to download the sequences of selected sno/scaRNAs in the FASTA format. The database is available online at http://www-snorna.biotoul.fr/. It can also be accessed from the human UCSC Genome Browser via the sno/miRNA track.

Figure 1

Sample of snoRNA-LBME-db entry. Hyperlinks are provided with GenBank, the UCSC Genome Browser and PubMed.

Figure 2

Sample of snoRNA annotation on the human UCSC Genome Browser. C/D and H/ACA box snoRNAs are colored dark gray and light gray, respectively; and scaRNAs, white (not shown). In the case of the cluster shown, the examination of the Hu/Chimp/Mouse/Rat/Dog/Chick/Fugu/Zfish Multiz Alignment & Conservation track reveals that sequences corresponding to snoRNAs are more conserved than those of the exons of the putative host gene.