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

By Laurent Lestrade, Michel J. Weber. Nucleic Acids Res., 2005

526 citations recorded by the source corpus.

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 . It can also be accessed from the human UCSC Genome Browser via the sno/miRNA track.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/42d2094f74f42534a7b0d82cd61db41fae81ef37

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Citations in the corpus

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes (2020, unknown): “This led to a minimum cohort size criterion of 20 patients, and removed the Bone-Cart (9 donors), Bone-Epith (11), BoneOsteoblast (5), Breast-DCIS (3), Breast-LobularCa (13), Cervix-AdenoCa (2), Cervix-SCC (18), CNS-Oligo (18), Lymph-NOS (2), Myeloid-AML (13) and Myeloid-MDS (2) individual cohorts.”
starBase: a database for exploring microRNA–mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data (2010, unknown): “Known non-coding RNA genes were downloaded from Ensembl (38) or UCSC (30) or were obtained from related literature (39–41).”
MODOMICS: a database of RNA modification pathways—2013 update (2012, methodology): “For this section of MODOMICS, we used data from the Saccharomyces Genome Database (42), the Yeast snoRNA Database (43) and snoRNA-LBME-db (44).”
Non-coding RNAs: lessons from the small nuclear and small nucleolar RNAs (2007, background): “Functional diversity and anatomy of the RNAs Whereas eukaryotic cells contain fewer than a dozen snRNA species, they contain more than 200 unique C/D and H/ACA RNA”
Identification and Classification of Conserved RNA Secondary Structures in the Human Genome (2006, background): “0 [47] that overlaps histone-associated transcripts (as defined by the known gene annotation of the UCSC Human Genome Browser [65]); the set of human tRNAs as defined by tRNAscan-SE predictions scoring above 55 bits [66]; the set of snoRNAs defined in snoRNA-LBME-db [67]; and against the more broadl”
Human box C/D snoRNAs with miRNA like functions: expanding the range of regulatory RNAs (2010, methodology): “To confirm that this feature is a general property, we scanned all 402 snoRNAs in snoRNABase version 3 (37) and found 107 candidates where (i) the box C element (UGUGUA) occurs inside an expressed subsequence and/or (ii) the box D element (CUGA) is flanking (and often partly contained in) the small ”
Rfam: Wikipedia, clans and the “decimal” release (2010, methodology): “For the snoRNAs, we used some of the specialized snoRNA databases to conﬁrm whether families targeted orthologous regions of rRNA, for many snoRNAs this helped to conﬁrm a relationship between the families (20–23).”
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures (2007, background): “The predictions also included nine novel H/ACA-box small nucleolar RNA candidates in introns of ribosomal genes, known to frequently contain small nucleolar RNAs that guide post-transcriptional base modifications of ncRNAs 67 .”
Rfam: updates to the RNA families database (2008, methodology): “We have been actively updating Rfam families and database crosslinks using more specialized RNA databases such as miRBase (18), IRESite (19), Pseudobase (20), snoRNABase (21), the plant snoRNA database (22), TransTerm (23) and the Yeast snoRNA database (24).”
A human snoRNA with microRNA-like functions. (2008, methodology): “Human snoRNA sequences were downloaded from snoRNABase (Lestrade and Weber, 2006).”