title: Swinger RNAs with sharp switches between regular transcription and transcription systematically exchanging ribonucleotides: Case studies.
abstract: During RNA transcription, DNA nucleotides A,C,G, T are usually matched by ribonucleotides A, C, G and U. However occasionally, this rule does not apply: transcript-DNA homologies are detectable only assuming systematic exchanges between ribonucleotides. Nine symmetric (X ↔ Y, e.g. A ↔ C) and fourteen asymmetric (X ↔ Y ↔ Z, e.g. A ↔ C ↔ G) exchanges exist, called swinger transcriptions. Putatively, polymerases occasionally stabilize in unspecified swinger conformations, possibly similar to transient conformations causing punctual misinsertions. This predicts chimeric transcripts, part regular, part swinger-transformed, reflecting polymerases switching to swinger polymerization conformation(s). Four chimeric Genbank transcripts (three from human mitochondrion and one murine cytosolic) are described here: (a) the 5' and 3' extremities reflect regular polymerization, the intervening sequence exchanges systematically between ribonucleotides (swinger rule G ↔ U, transcript (1), with sharp switches between regular and swinger sequences; (b) the 5' half is 'normal', the 3' half systematically exchanges ribonucleotides (swinger rule C ↔ G, transcript (2), with an intercalated sequence lacking homology; (c) the 3' extremity fits A ↔ G exchanges (10% of transcript length), the 5' half follows regular transcription; the intervening region seems a mix of regular and A ↔ G transcriptions (transcript 3); (d) murine cytosolic transcript 4 switches to A ↔ U + C ↔ G, and is fused with A ↔ U + C ↔ G swinger transformed precursor rRNA. In (c), each concomitant transcript 5' and 3' extremities match opposite genome strands. Transcripts 3 and 4 combine transcript fusions with partial swinger transcriptions. Occasional (usually sharp) switches between regular and swinger transcriptions reveal greater coding potential than detected until now, suggest stable polymerase swinger conformations.
authors.affiliation: Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes, Faculté de Médecine, URMITE CNRS-IRD 198 UMR 6236, Université d'Aix-Marseille, Marseille, France. Electronic address: varanuseremius@gmail.com.
authors.forename: Hervé
authors.initials: H
authors.lastname: Seligmann
mesh_terms: D000818:Animals; D001483:Base Sequence; D046528:Chimerism; D030561:Databases, Nucleic Acid; D006801:Humans; D051379:Mice; D008969:Molecular Sequence Data; D058105:Polymerization; D012313:RNA; D012265:Ribonucleotides; D014158:Transcription, Genetic
chemical_list: D012265:Ribonucleotides; D012313:RNA
keywords: Nucleotide misinsertion; Polymerase fidelity; RNA elongation; Swinger polymerization; Systematic nucleotide exchange; Transcription