Swinger RNAs with sharp switches between regular transcription and transcription systematically exchanging ribonucleotides: Case studies

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.