Combined experimental and computational approach to identify non-protein-coding 
RNAs in the deep-branching eukaryote Giardia intestinalis

Chen, Xiaowei Sylvia; Rozhdestvensky, Timofey S.; Collins, Lesley J.; Schmitz, Jurgen; Penny, David

doi:10.1093/nar/gkm474

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Combined experimental and computational approach to identify non-protein-coding RNAs in the deep-branching eukaryote Giardia intestinalis

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http://nar.oxfordjournals.org/content/35/14/4619/suppl/DC1
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NAR_ncRNA_Giardia_2007.pdf
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Citation

Chen, X. S., Rozhdestvensky, T. S., Collins, L. J., Schmitz, J., & Penny, D. (2007). Combined experimental and computational approach to identify non-protein-coding RNAs in the deep-branching eukaryote Giardia intestinalis. Nucleic Acids Research, 35, 4619-4628. doi:10.1093/nar/gkm474.

Cite as: https://hdl.handle.net/11858/00-001M-0000-000F-E5CA-2

Abstract

Non-protein-coding RNAs represent a large proportion of transcribed sequences in eukaryotes. These RNAs often function in large RNA–protein complexes, which are catalysts in various RNA-processing pathways. As RNA processing has become an increasingly important area of research, numerous non-messenger RNAs have been uncovered in all the model eukaryotic organisms. However, knowledge on RNA processing in deep-branching eukaryotes is still limited. This study focuses on the identification of non-protein-coding RNAs from the diplomonad parasite Giardia intestinalis, showing that a combined experimental and computational search strategy is a fast method of screening reduced or compact genomes. The analysis of our Giardia cDNA library has uncovered 31 novel candidates, including C/D-box and H/ACA box snoRNAs, as well as an unusual transcript of RNase P, and double-stranded RNAs. Subsequent computational analysis has revealed additional putative C/D-box snoRNAs. Our results will lead towards a future understanding of RNA metabolism in the deep-branching eukaryote Giardia, as more ncRNAs are characterized.