Eukaryotic Cell doi:10.1128/EC.00296-06
Copyright (c) 2006, American Society for Microbiology and/or the Listed Authors/Institutions. All Rights Reserved.
A 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
* To whom correspondence should be addressed. Email:
michaes{at}mail.biu.ac.il.
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Abstract |
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Small nucleolar RNAs (snoRNA) are a large group of non-coding 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 in 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 RNA that can potentially guide 30 pseudouridinylation reactions. As in T. brucei, Leishmania also contain many modifications and guide RNAs, relative to their genome size. This study describes 10 H/ACA and 14 C/D 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 snoRNA such as copy number, conservation of the boxes, K-turn, intragenic and extragenic base-pairing were examined to elucidate the great variation among snoRNA abundance. This study highlights the power of comparative genomics for determining conserved features in non-coding RNAs.
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