title: Evolution of tRNA-like sequences and genome variability.
abstract: Transfer RNA (tRNA)-like sequences were searched for in the nine basic taxonomic divisions of GenBank-121 (viruses, phages, bacteria, plants, invertebrates, vertebrates, rodents, mammals, and primates) by an original program package implementing a dynamic profile alignment approach for the genetic texts' analysis, in using 22 profiles of tRNAs of different isotypes. In total, 175,901 previously unknown tRNA-like sequences were revealed. The locations of the tRNA-likes were considered over the regions whose functional meaning is described by standard Feature Keys in GenBank. Many regions containing the tRNA-like sequences were recognized as known repeats. A mode of distribution of the tRNA-like sequences in a genome was proposed as expansion in a content of the various transposable elements. An analysis of the integrity of RNA polymerase III inner promoters in the tRNA-like sequences over the GenBank divisions has shown a high possibility of generating new copies of short interspersed nuclear element (SINE) repeats in all divisions, excepting primates. The numerous tRNA-likes found in the regions of RNA polymerase II promoters have suggested an adaptation of RNA polymerase III promoter to a binding of RNA polymerase II.
authors.affiliation: Centre Bioengineering RAS, Prospekt 60-letiya Oktyabrya, 7/1, Moscow 117312, Russia. felix@biengi.ac.ru
authors.forename: Felix E
authors.initials: FE
authors.lastname: Frenkel
authors.forename: Maria B
authors.initials: MB
authors.lastname: Chaley
authors.forename: Eugene V
authors.initials: EV
authors.lastname: Korotkov
authors.forename: Konstantin G
authors.initials: KG
authors.lastname: Skryabin
mesh_terms: D000465:Algorithms; D000818:Animals; D001482:Base Composition; D001483:Base Sequence; D004247:DNA / Q000737:chemistry / Q000235:genetics*; D004251:DNA Transposable Elements / Q000235:genetics; D030561:Databases, Nucleic Acid; D005057:Eukaryotic Cells / Q000378:metabolism; D019143:Evolution, Molecular; D014644:Genetic Variation; D016678:Genome; D006801:Humans; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011387:Prokaryotic Cells / Q000378:metabolism; D012343:RNA, Transfer / Q000737:chemistry / Q000235:genetics; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods
chemical_list: D004251:DNA Transposable Elements; D004247:DNA; D012343:RNA, Transfer