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Nucleic Acids Research, 2003, Vol. 31, No. 10 2495-2507
© 2003 Oxford University Press

RNomics in Drosophila melanogaster: identification of 66 candidates for novel non-messenger RNAs

Guozhong Yuan, Christian Klämbt1, Jean-Pierre Bachellerie2, Jürgen Brosius and Alexander Hüttenhofer

Institute for Experimental Pathology (ZMBE), 1 Institute for Zoology, Universität Münster, D-48149 Münster, Germany and 2 Laboratoire de Biologie Moleculaire Eucaryote du CNRS, Universite Paul-Sabatier, 118 route de Narbonne, F-31062 Toulouse cedex 04, France

*To whom correspondence should be addressed at present address: Institute for Molecular Biology, Department of Functional Genomics, Fritz-Pregl-Str. 3, A-6020 Austria. Tel: +43 512 507 3630; Fax: +43 512 507 9880; Email: alexander.huettenhofer{at}uibk.ac.at

Correspondence may also be addressed to Jean-Pierre Bachellerie. Tel: +33 5 61 33 59 34; Fax: +33 5 61 33 58 86; Email: bachel{at}ibcg.biotoul.fr

By generating a specialised cDNA library from four different developmental stages of Drosophila melanogaster, we have identified 66 candidates for small non-messenger RNAs (snmRNAs) and have confirmed their expression by northern blot analysis. Thirteen of them were expressed at certain stages of D.melanogaster development, only. Thirty-five species belong to the class of small nucleolar RNAs (snoRNAs), divided into 15 members from the C/D subclass and 20 members from the H/ACA subclass, which mostly guide 2'-O-methylation and pseudouridylation, respectively, of rRNA and snRNAs. These also include two outstanding C/D snoRNAs, U3 and U14, both functioning as pre-rRNA chaperones. Surprisingly, the sequence of the Drosophila U14 snoRNA reflects a major change of function of this snoRNA in Diptera relative to yeast and vertebrates. Among the 22 snmRNAs lacking known sequence and structure motifs, five were located in intergenic regions, two in introns, five in untranslated regions of mRNAs, eight were derived from open reading frames, and two were transcribed opposite to an intron. Interestingly, detection of two RNA species from this group implies that certain snmRNA species are processed from alternatively spliced pre-mRNAs. Surprisingly, a few snmRNA sequences could not be found on the published D.melanogaster genome, which might suggest that more snmRNA genes (as well as mRNAs) are hidden in unsequenced regions of the genome.


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