Genome-wide analysis of small nucleolar RNAs of Leishmania major reveals a rich repertoire of RNAs involved in modification and processing of rRNA

RNA Biol. 2015;12(11):1222-55. doi: 10.1080/15476286.2015.1038019. Epub 2015 May 13.

Abstract

Trypanosomatids are protozoan parasites and the causative agent of infamous infectious diseases. These organisms regulate their gene expression mainly at the post-transcriptional level and possess characteristic RNA processing mechanisms. In this study, we analyzed the complete repertoire of Leishmania major small nucleolar (snoRNA) RNAs by performing RNA-seq analysis on RNAs that were affinity-purified using the C/D snoRNA core protein, SNU13, and the H/ACA core protein, NHP2. This study revealed a large collection of C/D and H/ACA snoRNAs, organized in gene clusters generally containing both snoRNA types. Abundant snoRNAs were identified and predicted to guide trypanosome-specific rRNA cleavages. The repertoire of snoRNAs was compared to that of the closely related Trypanosoma brucei, and 80% of both C/D and H/ACA molecules were found to have functional homologues. The comparative analyses elucidated how snoRNAs evolved to generate molecules with analogous functions in both species. Interestingly, H/ACA RNAs have great flexibility in their ability to guide modifications, and several of the RNA species can guide more than one modification, compensating for the presence of single hairpin H/ACA snoRNA in these organisms. Placing the predicted modifications on the rRNA secondary structure revealed hypermodification regions mostly in domains which are modified in other eukaryotes, in addition to trypanosome-specific modifications.

Keywords: C/D; H/ACA; Leishmania; methylation; pseudouridylation; rRNA processing; snoRNA.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Pairing
  • Base Sequence
  • Binding Sites
  • Gene Library
  • Genome, Protozoan*
  • Genome-Wide Association Study*
  • Leishmania major / genetics*
  • Leishmania major / metabolism
  • Multigene Family
  • Nucleic Acid Conformation
  • RNA Processing, Post-Transcriptional*
  • RNA, Ribosomal / chemistry
  • RNA, Ribosomal / genetics*
  • RNA, Ribosomal / metabolism
  • RNA, Small Nucleolar / chemistry
  • RNA, Small Nucleolar / genetics*
  • RNA, Small Nucleolar / metabolism
  • Ribonucleoproteins, Small Nuclear / metabolism
  • Trypanosoma / genetics
  • Trypanosoma / metabolism

Substances

  • RNA, Ribosomal
  • RNA, Small Nucleolar
  • Ribonucleoproteins, Small Nuclear