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 (original) (raw)
- XUE-HAI LIANG1,2,
- SHAI ULIEL1,2,
- AVRAHAM HURY1,
- SARIT BARTH1,
- TIRZA DONIGER1,
- RON UNGER1, and
- SHULAMIT MICHAELI1
- 1Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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, ~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.
Footnotes
↵2 These authors contributed equally to this work.
Article and publication are at http://www.rnajournal.org/cgi/doi/10.1261/rna.7174805.
- Accepted January 17, 2005.
- Received September 2, 2004.
Copyright 2005 by RNA Society