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

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          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.

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          Author and article information

          Journal
          RNA Biol
          RNA biology
          Informa UK Limited
          1555-8584
          1547-6286
          2015
          : 12
          : 11
          Affiliations
          [1 ] a The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute ; Bar-Ilan University ; Ramat-Gan , Israel.
          [2 ] b Department of Epidemiology of Microbial Diseases ; Yale University School of Public Health ; New Haven , CT USA.
          [3 ] c Department of Internal Medicine and Cell Biology ; Yale University Medical School ; New Haven , CT USA.
          [4 ] d Cell Biology ; Yale University Medical School ; New Haven , CT USA.
          Article
          10.1080/15476286.2015.1038019
          4829279
          25970223
          85e76b24-19ac-4049-b9c7-a5ad5141c413
          History

          C/D,H/ACA,Leishmania,methylation,pseudouridylation,rRNA processing,snoRNA

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