title: Combined experimental and computational approach to identify non-protein-coding RNAs in the deep-branching eukaryote Giardia intestinalis.
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.
authors.affiliation: Allan Wilson Centre, IMBS, Massey University, Palmerston North, New Zealand.
authors.forename: Xiaowei Sylvia
authors.initials: XS
authors.lastname: Chen
authors.forename: Timofey S
authors.initials: TS
authors.lastname: Rozhdestvensky
authors.forename: Lesley J
authors.initials: LJ
authors.lastname: Collins
authors.forename: Jürgen
authors.initials: J
authors.lastname: Schmitz
authors.forename: David
authors.initials: D
authors.lastname: Penny
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods; D018076:DNA, Complementary / Q000737:chemistry; D015723:Gene Library; D016829:Giardia lamblia / Q000235:genetics*; D016053:RNA, Protozoan / Q000737:chemistry*; D020537:RNA, Small Nucleolar / Q000737:chemistry; D022661:RNA, Untranslated / Q000737:chemistry*; D012091:Repetitive Sequences, Nucleic Acid; D043262:Ribonuclease P / Q000737:chemistry; D017423:Sequence Analysis, RNA
chemical_list: D018076:DNA, Complementary; D016053:RNA, Protozoan; D020537:RNA, Small Nucleolar; D022661:RNA, Untranslated; D043262:Ribonuclease P