Published in:  Nucleic Acids Research, vol. 31, no. 10, pp. 2495-2507 (May 15, 2003).

http://nar.oupjournals.org/cgi/content/abstract/31/10/2495?etoc

"RNomics in Drosophila melanogaster: Identification of 66 Candidates for Novel Non-messenger RNAs".

Guozhong Yuan, Christian Klämbt 1, Jean-Pierre Bachellerie 2 , 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

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@ibcg.biotoul.fr


Abstract:

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. 


Database of Small Non-Messenger RNAs (snmRNAs):
(Part of Institute of Experimental Pathology/Molecular Neurobiology website.)
http://exppc01.uni-muenster.de/expath/snmrnas.htm

Compilation of novel ERNS from Fraction I (derived from RNAs sized 500-110 nts) and Fraction II (derived from RNAs sized 110-50 nts) cDNA libraries:
 

  • ERNS: expressed RNA sequences from Fraction I (MBI-) or Fraction II (MBII-);
  • copies: number of independent cDNA clones identified from each RNA species;
  • cDNA: length of cDNA, as assessed by sequencing;
  • RNA: length of RNA as assessed by Northern blot analysis;
  • homology: homology of snmRNAs to genomic or EST sequences within other organisms;
  • modification: predicted modified nucleotides within rRNAs or snRNAs (numbering according to the human RNA sequence);
  • antisense element: for C/D box snoRNAs the length of the antisense element is indicated in nucleotides, followed by its location in the 5' domain (5') or 3' domain (3') of the snoRNA;
  • location / comments: genomic locus and specific features of ERNS (when applicable);
  • Acc. Nr.: accession number in GenBank.



    • Additional References:

    1. Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H, Bachellerie J-P, and Brosius J, "RNomics: An Experimental Approach that Identifies 201 Candidates for Novel, Small, Non-Messenger RNAs in Mouse".

    2. Muslimov IA, Lin Y, Heller M, Brosius J, Zakeri Z, and Tiedge H, "A Small RNA in Testis and Brain: Implications for Male Germ Cell Development".

    3. Saha S, Ansari AZ, Jarell KA, and Ptashne M, "RNA Sequences that Work as Transcriptional Activating Regions".

    4. Hovsepian JA, and Frenster JH, "RNA-Induced Melting of DNA during Selective Gene Transcription".

    5. Frenster JH, "Ultrastructural Probes of Active DNA Sites, and the RNA Activators of DNA".

    Top of Page - Euchromatin Network - Current Research - Forums - Other Sites - Future Events -


    For Further Information or Feedback:
    e-mail:   frenster@euchromatin.net
    Phone:   +1 650 367 6483
    Fax:   +1 650 364 1773

    euchromatin:  "the most active portion of the genome within the cell nucleus".