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  Computational identification of four spliceosomal snRNAs from the deep-branch eukaryote Giardia intestinalis

Chen, X. S., White, W. T. J., Collins, L. J., & Penny, D. (2008). Computational identification of four spliceosomal snRNAs from the deep-branch eukaryote Giardia intestinalis. PLoS One, 3(8), e3106. doi:10.1371/journal.pone.0003106.

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computational_snRNA_plosone.pdf (Verlagsversion), 333KB
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computational_snRNA_plosone.pdf
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 Urheber:
Chen, Xiaowei Sylvia1, Autor           
White, W. Timothy J.1, Autor
Collins, Lesley J.1, Autor
Penny, David1, Autor
Affiliations:
1Allan Wilson Centre for Molecular Ecology and Evolution, IMBS, Massey University, Palmerston North, New Zealand, ou_persistent22              

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 Zusammenfassung: RNAs processing other RNAs is very general in eukaryotes, but is not clear to what extent it is ancestral to eukaryotes. Here we focus on pre-mRNA splicing, one of the most important RNA-processing mechanisms in eukaryotes. In most eukaryotes splicing is predominantly catalysed by the major spliceosome complex, which consists of five uridine-rich small nuclear RNAs (U-snRNAs) and over 200 proteins in humans. Three major spliceosomal introns have been found experimentally in Giardia; one Giardia U-snRNA (U5) and a number of spliceosomal proteins have also been identified. However, because of the low sequence similarity between the Giardia ncRNAs and those of other eukaryotes, the other U-snRNAs of Giardia had not been found. Using two computational methods, candidates for Giardia U1, U2, U4 and U6 snRNAs were identified in this study and shown by RT-PCR to be expressed. We found that identifying a U2 candidate helped identify U6 and U4 based on interactions between them. Secondary structural modelling of the Giardia U-snRNA candidates revealed typical features of eukaryotic U-snRNAs. We demonstrate a successful approach to combine computational and experimental methods to identify expected ncRNAs in a highly divergent protist genome. Our findings reinforce the conclusion that spliceosomal small-nuclear RNAs existed in the last common ancestor of eukaryotes.

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Sprache(n): eng - English
 Datum: 2008-08-112008
 Publikationsstatus: Erschienen
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 Art der Begutachtung: Expertenbegutachtung
 Identifikatoren: DOI: 10.1371/journal.pone.0003106
PMC: PMC2518118
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Titel: PLoS One
Genre der Quelle: Zeitschrift
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Ort, Verlag, Ausgabe: San Francisco, CA : Public Library of Science
Seiten: 9 Band / Heft: 3 (8) Artikelnummer: - Start- / Endseite: e3106 Identifikator: ISSN: 1932-6203
CoNE: https://pure.mpg.de/cone/journals/resource/1000000000277850