Plant U13 orthologues and orphan snoRNAs identified by RNomics of RNA from Arabidopsis nucleoli

Sang Hyon Kim, Mark Spensley, Seung Kook Choi, Cristiane P. G. Calixto, Ali F. Pendle, Olga Koroleva, Peter J. Shaw, John W. S. Brown

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    Abstract

    Small nucleolar RNAs (snoRNAs) and small Cajal body-specific RNAs (scaRNAs) are non-coding RNAs whose main function in eukaryotes is to guide the modification of nucleotides in ribosomal and spliceosomal small nuclear RNAs, respectively. Full-length sequences of Arabidopsis snoRNAs and scaRNAs have been obtained from cDNA libraries of capped and uncapped small RNAs using RNA from isolated nucleoli from Arabidopsis cell cultures. We have identified 31 novel snoRNA genes (9 box C/D and 22 box H/ACA) and 15 new variants of previously described snoRNAs. Three related capped snoRNAs with a distinct gene organization and structure were identified as orthologues of animal U13snoRNAs. In addition, eight of the novel genes had no complementarity to rRNAs or snRNAs and are therefore putative orphan snoRNAs potentially reflecting wider functions for these RNAs. The nucleolar localization of a number of the snoRNAs and the localization to nuclear bodies of two putative scaRNAs was confirmed by in situ hybridization. The majority of the novel snoRNA genes were found in new gene clusters or as part of previously described clusters. These results expand the repertoire of Arabidopsis snoRNAs to 188 snoRNA genes with 294 gene variants.

    Original languageEnglish
    Pages (from-to)3054-3067
    Number of pages14
    JournalNucleic Acids Research
    Volume38
    Issue number9
    DOIs
    Publication statusPublished - May 2010

    Cite this

    Kim, S. H., Spensley, M., Choi, S. K., Calixto, C. P. G., Pendle, A. F., Koroleva, O., Shaw, P. J., & Brown, J. W. S. (2010). Plant U13 orthologues and orphan snoRNAs identified by RNomics of RNA from Arabidopsis nucleoli. Nucleic Acids Research, 38(9), 3054-3067. https://doi.org/10.1093/nar/gkp1241