Characterization of RNase MRP RNA and novel snoRNAs from Giardia intestinalis and Trichomonas vaginalis

Xiaowei S Chen,Lesley J Collins,David Penny

doi:10.1186/1471-2164-12-550

Xiaowei S Chen, Lesley J Collins + Show 1 more

Open Access

https://doi.org/10.1186/1471-2164-12-550

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Journal: BMC Genomics	Publication Date: Nov 6, 2011
Citations: 59	License type: cc-by

Affiliation: University of Otago, Massey University

Abstract

BackgroundEukaryotic cells possess a complex network of RNA machineries which function in RNA-processing and cellular regulation which includes transcription, translation, silencing, editing and epigenetic control. Studies of model organisms have shown that many ncRNAs of the RNA-infrastructure are highly conserved, but little is known from non-model protists. In this study we have conducted a genome-scale survey of medium-length ncRNAs from the protozoan parasites Giardia intestinalis and Trichomonas vaginalis.ResultsWe have identified the previously 'missing' Giardia RNase MRP RNA, which is a key ribozyme involved in pre-rRNA processing. We have also uncovered 18 new H/ACA box snoRNAs, expanding our knowledge of the H/ACA family of snoRNAs.ConclusionsResults indicate that Giardia intestinalis and Trichomonas vaginalis, like their distant multicellular relatives, contain a rich infrastructure of RNA-based processing. From here we can investigate the evolution of RNA processing networks in eukaryotes.

Highlights

Eukaryotic cells possess a complex network of RNA machineries which function in RNA-processing and cellular regulation which includes transcription, translation, silencing, editing and epigenetic control
In contrast to the genomewide transcriptional information known in other eukaryotic models, only limited information on RNA biology is available from G. intestinalis and T. vaginalis
In this study we identify medium-length ncRNAs (50-250 nt) from small RNA based sequencing data, characterize the RNase MRP of G. intestinalis, and clarify annotations of RNase P and MRP from both G. intestinalis and T. vaginalis

Summary

Introduction

Eukaryotic cells possess a complex network of RNA machineries which function in RNA-processing and cellular regulation which includes transcription, translation, silencing, editing and epigenetic control. In this study we have conducted a genome-scale survey of medium-length ncRNAs from the protozoan parasites Giardia intestinalis and Trichomonas vaginalis. Studies on Trichomonas ncRNAs show that the currently known ncRNAs exhibit typical features of eukaryotes [8,16,17,18] including RNase P [8], RNase MRP [8], snRNAs [17] and some snoRNAs [9,14]. There are still gaps in our knowledge of RNA processing in these species, especially in the characterization of the RNase MRP RNA in Giardia, and the different types of snoRNAs in Trichomonas (Figure 1). We characterize medium length ncRNAs including RNase MRP, RNase P and snoRNAs from two protozoan parasites: Giardia intestinalis (Diplomonad) and Trichomonas vaginalis (Parabasalid), to clarify uncertainties about conserved features of the RNA infrastructure

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