title: Prediction of structured non-coding RNAs in the genomes of the nematodes Caenorhabditis elegans and Caenorhabditis briggsae.
abstract: We present a survey for non-coding RNAs and other structured RNA motifs in the genomes of Caenorhabditis elegans and Caenorhabditis briggsae using the RNAz program. This approach explicitly evaluates comparative sequence information to detect stabilizing selection acting on RNA secondary structure. We detect 3,672 structured RNA motifs, of which only 678 are known non-translated RNAs (ncRNAs) or clear homologs of known C. elegans ncRNAs. Most of these signals are located in introns or at a distance from known protein-coding genes. With an estimated false positive rate of about 50% and a sensitivity on the order of 50%, we estimate that the nematode genomes contain between 3,000 and 4,000 RNAs with evolutionary conserved secondary structures. Only a small fraction of these belongs to the known RNA classes, including tRNAs, snoRNAs, snRNAs, or microRNAs. A relatively small class of ncRNA candidates is associated with previously observed RNA-specific upstream elements.
authors.affiliation: Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16 18, D 04107 Leipzig, Germany. kristin@bioinf.uni-leipzig.de
authors.forename: Kristin
authors.initials: K
authors.lastname: Missal
authors.forename: Xiaopeng
authors.initials: X
authors.lastname: Zhu
authors.forename: Dominic
authors.initials: D
authors.lastname: Rose
authors.forename: Wei
authors.initials: W
authors.lastname: Deng
authors.forename: Geir
authors.initials: G
authors.lastname: Skogerbø
authors.forename: Runsheng
authors.initials: R
authors.lastname: Chen
authors.forename: Peter F
authors.initials: PF
authors.lastname: Stadler
mesh_terms: D000818:Animals; D002107:Caenorhabditis / Q000235:genetics*; D017173:Caenorhabditis elegans / Q000235:genetics; D049751:Genome, Helminth / Q000235:genetics*; D007438:Introns / Q000235:genetics; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics; D009690:Nucleic Acid Conformation; D011401:Promoter Regions, Genetic / Q000235:genetics; D018510:RNA, Helminth / Q000737:chemistry* / Q000235:genetics*; D022661:RNA, Untranslated / Q000235:genetics*; D012680:Sensitivity and Specificity; D016415:Sequence Alignment
chemical_list: D035683:MicroRNAs; D018510:RNA, Helminth; D022661:RNA, Untranslated