title: The distribution of RNA motifs in natural sequences.
abstract: Functional analysis of genome sequences has largely ignored RNA genes and their structures. We introduce here the notion of 'ribonomics' to describe the search for the distribution of and eventually the determination of the physiological roles of these RNA structures found in the sequence databases. The utility of this approach is illustrated here by the identification in the GenBank database of RNA motifs having known binding or chemical activity. The frequency of these motifs indicates that most have originated from evolutionary drift and are selectively neutral. On the other hand, their distribution among species and their location within genes suggest that the destiny of these motifs may be more elaborate. For example, the hammerhead motif has a skewed organismal presence, is phylogenetically stable and recent work on a schistosome version confirms its in vivo biological activity. The under-representation of the valine-binding motif and the Rev-binding element in GenBank hints at a detrimental effect on cell growth or viability. Data on the presence and the location of these motifs may provide critical guidance in the design of experiments directed towards the understanding and the manipulation of RNA complexes and activities in vivo.
authors.affiliation: Département de Biochimie, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC H3C 3J7, Canada.
authors.forename: V
authors.initials: V
authors.lastname: Bourdeau
authors.forename: G
authors.initials: G
authors.lastname: Ferbeyre
authors.forename: M
authors.initials: M
authors.lastname: Pageau
authors.forename: B
authors.initials: B
authors.lastname: Paquin
authors.forename: R
authors.initials: R
authors.lastname: Cedergren
mesh_terms: D000255:Adenosine Triphosphate / Q000378:metabolism; D001483:Base Sequence; D001665:Binding Sites; D020134:Catalytic Domain; D016208:Databases, Factual; D019143:Evolution, Molecular; D005486:Flavin Mononucleotide / Q000378:metabolism; D005182:Flavin-Adenine Dinucleotide / Q000378:metabolism; D015694:Gene Products, rev / Q000378:metabolism; D015696:Gene Products, tat / Q000378:metabolism; D016247:Information Storage and Retrieval; D008024:Ligands; D008969:Molecular Sequence Data; D009355:Neomycin / Q000378:metabolism; D009690:Nucleic Acid Conformation; D010303:Paromomycin / Q000378:metabolism; D010802:Phylogeny; D012313:RNA / Q000737:chemistry* / Q000378:metabolism; D016337:RNA, Catalytic / Q000737:chemistry; D012343:RNA, Transfer / Q000737:chemistry; D016601:RNA-Binding Proteins / Q000378:metabolism*; D012269:Ribosomal Proteins / Q000378:metabolism; D013806:Theophylline / Q000378:metabolism
chemical_list: D015694:Gene Products, rev; D015696:Gene Products, tat; D008024:Ligands; D016337:RNA, Catalytic; D016601:RNA-Binding Proteins; D012269:Ribosomal Proteins; C113411:leadzyme; C015494:ribosomal protein S1; D005182:Flavin-Adenine Dinucleotide; D010303:Paromomycin; D012313:RNA; D005486:Flavin Mononucleotide; D000255:Adenosine Triphosphate; D012343:RNA, Transfer; D013806:Theophylline; D009355:Neomycin