title: Experimental RNomics: identification of 140 candidates for small non-messenger RNAs in the plant Arabidopsis thaliana.
abstract: BACKGROUND
  Genomes from all organisms known to date express two types of RNA molecules: messenger RNAs (mRNAs), which are translated into proteins, and non-messenger RNAs, which function at the RNA level and do not serve as templates for translation.
  
  
  RESULTS
  We have generated a specialized cDNA library from Arabidopsis thaliana to investigate the population of small non-messenger RNAs (snmRNAs) sized 50-500 nt in a plant. From this library, we identified 140 candidates for novel snmRNAs and investigated their expression, abundance, and developmental regulation. Based on conserved sequence and structure motifs, 104 snmRNA species can be assigned to novel members of known classes of RNAs (designated Class I snmRNAs), namely, small nucleolar RNAs (snoRNAs), 7SL RNA, U snRNAs, as well as a tRNA-like RNA. For the first time, 39 novel members of H/ACA box snoRNAs could be identified in a plant species. Of the remaining 36 snmRNA candidates (designated Class II snmRNAs), no sequence or structure motifs were present that would enable an assignment to a known class of RNAs. These RNAs were classified based on their location on the A. thaliana genome. From these, 29 snmRNA species located to intergenic regions, 3 located to intronic sequences of protein coding genes, and 4 snmRNA candidates were derived from annotated open reading frames. Surprisingly, 15 of the Class II snmRNA candidates were shown to be tissue-specifically expressed, while 12 are encoded by the mitochondrial or chloroplast genome.
  
  
  CONCLUSIONS
  Our study has identified 140 novel candidates for small non-messenger RNA species in the plant A. thaliana and thereby sets the stage for their functional analysis.
authors.affiliation: Institute of Experimental Pathology, ZMBE, Von-Esmarch-Str 56, 48149 Münster, Germany.
authors.forename: Claudia
authors.initials: C
authors.lastname: Marker
authors.forename: Anja
authors.initials: A
authors.lastname: Zemann
authors.forename: Tanja
authors.initials: T
authors.lastname: Terhörst
authors.forename: Martin
authors.initials: M
authors.lastname: Kiefmann
authors.forename: James P
authors.initials: JP
authors.lastname: Kastenmayer
authors.forename: Pamela
authors.initials: P
authors.lastname: Green
authors.forename: Jean-Pierre
authors.initials: JP
authors.lastname: Bachellerie
authors.forename: Jürgen
authors.initials: J
authors.lastname: Brosius
authors.forename: Alexander
authors.initials: A
authors.lastname: Hüttenhofer
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D002736:Chloroplasts / Q000235:genetics; D015723:Gene Library; D018745:Genome, Plant; D008928:Mitochondria / Q000235:genetics; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D018749:RNA, Plant / Q000235:genetics*; D034741:RNA, Small Interfering / Q000235:genetics*
chemical_list: D018749:RNA, Plant; D034741:RNA, Small Interfering