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.
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.
Liang
Xue-Hai
XH
Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel.
Uliel
Shai
S
Hury
Avraham
A
Barth
Sarit
S
Doniger
Tirza
T
Unger
Ron
R
Michaeli
Shulamit
S
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*
D016053:RNA, Protozoan; D020537:RNA, Small Nucleolar