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.
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.
Liang
Xue-hai
XH
The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel.
Hury
Avraham
A
Hoze
Ehud
E
Uliel
Shai
S
Myslyuk
Inna
I
Apatoff
Avihay
A
Unger
Ron
R
Michaeli
Shulamit
S
D000818:Animals; D001483:Base Sequence; D019295:Computational Biology; D017124:Conserved Sequence; D005786:Gene Expression Regulation; D017125:Genes, Protozoan / Q000235:genetics*; D006801:Humans; D007891:Leishmania / Q000235:genetics*; D008745:Methylation; D011560:Pseudouridine / Q000378:metabolism; D016053:RNA, Protozoan / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D020537:RNA, Small Nucleolar / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D020718:Ribonucleoproteins, Small Nucleolar; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity; D013379:Substrate Specificity
D016053:RNA, Protozoan; D020537:RNA, Small Nucleolar; D020718:Ribonucleoproteins, Small Nucleolar; D011560:Pseudouridine