title: A genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in Trypanosoma brucei reveals a trypanosome-specific pattern of rRNA modification.
abstract: Small nucleolar RNAs (snoRNAs) constitute newly discovered noncoding small RNAs, most of which function in guiding modifications such as 2'-O-ribose methylation and pseudouridylation on rRNAs and snRNAs. To investigate the genome organization of Trypanosoma brucei snoRNAs and the pattern of rRNA modifications, we used a whole-genome approach to identify the repertoire of these guide RNAs. Twenty-one clusters encoding for 57 C/D snoRNAs and 34 H/ACA-like RNAs, which have the potential to direct 84 methylations and 32 pseudouridines, respectively, were identified. The number of 2'-O-methyls (Nms) identified on rRNA represent 80% of the expected modifications. The modifications guided by these RNAs suggest that trypanosomes contain many modifications and guide RNAs relative to their genome size. Interestingly, approximately 40% of the Nms are species-specific modifications that do not exist in yeast, humans, or plants, and 40% of the species-specific predicted modifications are located in unique positions outside the highly conserved domains. Although most of the guide RNAs were found in reiterated clusters, a few single-copy genes were identified. The large repertoire of modifications and guide RNAs in trypanosomes suggests that these modifications possibly play a central role in these parasites.
authors.affiliation: Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel.
authors.forename: Xue-Hai
authors.initials: XH
authors.lastname: Liang
authors.forename: Shai
authors.initials: S
authors.lastname: Uliel
authors.forename: Avraham
authors.initials: A
authors.lastname: Hury
authors.forename: Sarit
authors.initials: S
authors.lastname: Barth
authors.forename: Tirza
authors.initials: T
authors.lastname: Doniger
authors.forename: Ron
authors.initials: R
authors.lastname: Unger
authors.forename: Shulamit
authors.initials: S
authors.lastname: Michaeli
mesh_terms: D000818:Animals; D020029:Base Pairing; D001483:Base Sequence; D019295:Computational Biology; D017124:Conserved Sequence / Q000235:genetics; D005786:Gene Expression Regulation; D017125:Genes, Protozoan / Q000235:genetics; D018503:Genome, Protozoan; D023281:Genomics; D008969:Molecular Sequence Data; D005810:Multigene Family / Q000235:genetics; D016053:RNA, Protozoan / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D020537:RNA, Small Nucleolar / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D013045:Species Specificity; D013379:Substrate Specificity; D014346:Trypanosoma brucei brucei / Q000145:classification* / Q000235:genetics*
chemical_list: D016053:RNA, Protozoan; D020537:RNA, Small Nucleolar