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Nucleic Acids Research Advance Access originally published online on June 22, 2007
Nucleic Acids Research 2007 35(14):4619-4628; doi:10.1093/nar/gkm474
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Nucleic Acids Research, 2007, Vol. 35, No. 14 4619-4628
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

RNA

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

Xiaowei (Sylvia) Chen1, Timofey S. Rozhdestvensky2, Lesley J. Collins1,*, Jürgen Schmitz2 and David Penny1

1Allan Wilson Centre, IMBS, Massey University, Palmerston North, New Zealand and 2Institute of Experimental Pathology (ZMBE), University of Münster, Münster, Germany

*To whom correspondence should be addressed. Tel: +64 6 350 9099-7345; Fax: +64 6 350 5626; Email: l.j.collins{at}massey.ac.nz

Received February 8, 2007. Revised May 29, 2007. Accepted May 29, 2007.

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.


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