Swinger RNAs in the Human Mitochondrial Transcriptome

Abstract

Transcriptomes include coding and non-coding RNAs and RNA fragments with no apparent homology to parent genomes. Non-canonical transcriptions systematically transforming template DNA sequences along precise rules explain some transcripts. Among these systematic transformations, 23 systematic exchanges between nucleotides, i.e. 9 symmetric (X ↔ Y, e.g. C ↔ T) and 14 asymmetric (X → Y → Z → X, e.g. A → T → G → A) exchanges. Here, comparisons between mitochondrial swinger RNAs previously detected in a complete human transcriptome dataset (including cytosolic RNAs) and swinger RNAs detected in purified mitochondrial transcriptomic data (not including cytosolic RNAs) show high reproducibility and exclude cytosolic contaminations. These results based on next-generation sequencing Illumina technology confirm detections of mitochondrial swinger RNAs in GenBank's EST database sequenced by the classical Sanger method, assessing the existence of swinger polymerizations.

Directed Mutations Recode Mitochondrial Genes: From Regular to Stopless Genetic Codes

“…Further little known mechanisms increase numbers of proteins potentially coded by single sequences. Polymerization occasionally exchanges systematically between nucleotides during DNA replication [44][45][46] or RNA transcription [47][48][49][50][51][52][53] for long sequence stretches (23 exchange rules are possible, nine symmetric, e.g., A<>C, and fourteen asymmetric, e.g., A > C > G > A), producing swinger sequences. Swinger replication, in particular the double symmetric exchange A<>T + C<>G, seems most frequent for mitochondrial ribosomal RNAs [46].…”

Systematic Nucleotide Exchange Analysis of ESTs From the Human Cancer Genome Project Report: Origins of 347 Unknown ESTs Indicate Putative Transcription of Non-Coding Genomic Regions

“…Detected peptides matching translation of the swingertransformed mitogenome tend to map on detected swinger RNAs (Seligmann, 2016a;Seligmann, 2016b;Seligmann, 2016c;Seligmann, 2017a). These findings were further confirmed in purified mitochondrial transcriptomes (Warthi and Seligmann, 2018), rejecting the possibility of cytoplasmic contamination. Chimeric mitochondrial swinger RNAs also exist, partly following swinger polymerization and partly regular polymerization, with abrupt switches between these parts (Seligmann, 2015a;Seligmann, 2015b).…”

“…Sixty-six percent (33 ESTs) of the identified swinger RNAs were transcribed from the MT-ND region. A previous study showed bias for swinger transformation of MT-ND genes (Warthi and Seligmann, 2018). Interestingly, detection of swinger transformed DLGAP1 mRNAs (overexpressed~15× in neurons compared to other tissue cells; Fagerberg et al, 2014), in normal nervous tissue samples suggests that the swinger transformation is not directly associated with cancer but perhaps associated with highly expressed genes.…”

Identification of Noncanonical Transcripts Produced by Systematic Nucleotide Exchanges in HIV-Associated Centroblastic Lymphoma

“…S winger transformations (also called systematic nucleotide exchanges) are phenomena, in which particular nucleotides replace systematically other particular nucleotide(s) during transcription or replication, producing swinger RNAs (Seligmann, 2012(Seligmann, , 2013a(Seligmann, , 2013bWarthi and Seligmann, 2018) or swinger DNAs (Seligmann, 2014(Seligmann, , 2015a(Seligmann, , 2015b. Swinger DNA corresponding to the 16S rRNA gene was also found integrated in a complete mitogenome (Seligmann, 2014).…”

“…Swinger DNA corresponding to the 16S rRNA gene was also found integrated in a complete mitogenome (Seligmann, 2014). Swinger transformation A4T+C4G is one among 23 nonidentical bijective transformations (Seligmann, 2012(Seligmann, , 2013a(Seligmann, , 2013bWarthi and Seligmann, 2018). The A4T+C4G transformation means that thymines replace all adenines, adenines replace all thymines (A4T), cytosines replace all guanines, and guanines replace all cytosines (C4G) during transcription/replication.…”