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Eukaryotic Cell, March 2007, p. 361-377, Vol. 6, No. 3
1535-9778/07/$08.00+0     doi:10.1128/EC.00296-06
Copyright © 2007, American Society for Microbiology. All Rights Reserved.

Genome-Wide Analysis of C/D and H/ACA-Like Small Nucleolar RNAs in Leishmania major Indicates Conservation among Trypanosomatids in the Repertoire and in Their rRNA Targets ^,

Xue-hai Liang ,^, Avraham Hury, Ehud Hoze, Shai Uliel, Inna Myslyuk, Avihay Apatoff, Ron Unger, and Shulamit Michaeli^*

The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel

Received 13 September 2006/ Accepted 7 December 2006

Small nucleolar RNAs (snoRNAs) are a large group of noncoding RNAs that exist in eukaryotes and archaea and guide modifications such as 2'-O-ribose methylations and pseudouridylation on rRNAs and snRNAs. Recently, we described a genome-wide screening approach with Trypanosoma brucei that revealed over 90 guide RNAs. In this study, we extended this approach to analyze the repertoire of the closely related human pathogen Leishmania major. We describe 23 clusters that encode 62 C/Ds that can potentially guide 79 methylations and 37 H/ACA-like RNAs that can potentially guide 30 pseudouridylation reactions. Like T. brucei, Leishmania also contains many modifications and guide RNAs relative to its genome size. This study describes 10 H/ACAs and 14 C/Ds that were not found in T. brucei. Mapping of 2'-O-methylations in rRNA regions rich in modifications suggests the existence of trypanosomatid-specific modifications conserved in T. brucei and Leishmania. Structural features of C/D snoRNAs, such as copy number, conservation of boxes, K turns, and intragenic and extragenic base pairing, were examined to elucidate the great variation in snoRNA abundance. This study highlights the power of comparative genomics for determining conserved features of noncoding RNAs.

Published ahead of print on 22 December 2006.

Supplemental material for this article may be found at http://ec.asm.org/.

X.-H.L. and A.H. contributed equally to this study.

Present address: Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA.

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