**1. Introduction**

Transcription is an intracellular mechanism that produces RNA by DNA-dependant RNA polymerisation. RNAs coding for polypeptide chains are mRNAs translated by other transcription products, tRNAs and ribosomal RNAs. Some RNAs do not correspond to any DNA sequence in the genome, suggesting in some cases spontaneous emergence [1]. These RNAs remain usually unreported and are ignored. Similarly, proteomic data include numerous peptides that do not match canonical translation of predicted ORFs, but imply translation of stop

© 2016 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. © 2018 The Author(s). Licensee IntechOpen. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

codons [2–8] by tRNAs with anticodons matching stops [9–11] or by tRNAs with expanded anticodons [12–14]. Assuming fusion of different transcripts explains the origins of some of these non-canonical RNAs [15]. Some human RNAs matching exons differ from their DNA by specific changes, called RDDs (RNA-DNA differences) [16]. RDDs can be single nucleotide substitutions or deletions [17–19], presumably resulting from post-transcriptional edition [20, 21]. Some short transcripts correspond to mitochondrial DNA at the condition that one assumes mono- or dinucleotide deletions after each transcribed nucleotide triplet [22, 23]. Formation of secondary structures by del-transformed sequences apparently downregulates del-transcription itself or its products, delRNAs [24].

from single polymerisation events, probably by the same polymerase [43]. Peptides corre-

Swinger RNAs in the Human Mitochondrial Transcriptome

http://dx.doi.org/10.5772/intechopen.80805

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Secondary structure formation by swinger-transformed sequences associates with swinger RNA detection [45], suggesting regulation of swinger RNA processing by secondary struc-

Abundances of human mitochondrial swinger RNAs detected in GenBank's EST database [25, 26], originating from various sources using Sanger sequencing, are proportional to those detected in transcriptomic data produced by next-generation sequencing, Illumina technology [47]. Similarly, abundances and lengths of swinger RNAs detected in *Mimivirus*' transcriptome sequenced by 454 technology are proportional to those detected when using SOLID sequencing [01]. These analyses confirmed that swinger RNAs are not sequencing artefacts due to specific sequencing technologies, but data sources do not exclude contamination by cytosolic RNA. Here, we compare the previously described human mitochondrial swinger transcriptome [39] from a complete human transcriptome (including cytosolic RNAs) with the swinger transcriptome as detected in purified human mitochondrial lines [48]. Reproducibility of swinger RNA coverages of the human mitogenome would exclude sequencing artefacts and cytosolic contaminations as alternative explanations for hypothetical swinger RNAs. We predict (1) the detection of swinger RNAs from transcriptomic data extracted from purified mitochondrial lines and (2) high similarities between mitogenomic

We used GenBank's BLASTn ('somewhat similar sequences' with default alignment parameters) [49] for in-silico alignment searches between each of the 23 swinger-transformed versions of the human mitogenome (NC\_012920) and transcriptomic data in GenBank's Sequence Read Archive (SRA) (SRX084350-SRX084355 and SRX087285), sequenced by RNA-Seq, Illumina HiSeq 2500 technology [48]. Alignments with more than 80% identity were

Locations of detected swinger RNAs were recorded by mapping these RNAs on the human mitogenome. We analyse separately 17 mitogenomic regions: the D-loop, 2 ribosomal RNAs (12S and 16S), 13 protein-coding genes involved in the electron transport chain and the WANCY region (intragenic region between ND2 and CO1 that templates for tRNAs with cognate amino acids W, A, N, C and Y). Percentage coverages by detected swinger RNAs were calculated for each swinger transformation in each selected mitogenomic region and

tures, as observed for canonical mitochondrial RNAs, i.e. tRNA punctuation [46].

sponding to such chimeric RNAs also occur [44].

swinger RNA coverages described here and previously [39].

recorded and used as a swinger RNA candidate for further analysis.

**2.2. Mitogenomic gene coverage by swinger RNAs**

**2. Materials and methods**

**2.1. Detection of swinger RNAs**

used for further statistical analyses.

Another type of systematic transformation consists of 23 systematic exchanges between nucleotides, 9 symmetric (X ↔ Y, e.g. A ↔ C,) [25, 26] and 14 asymmetric exchanges (X → Y → Z → X, e.g. A → C → G → A) [26, 27]. For example, in systematic transformation A ↔ C, nucleotide A is introduced in place of nucleotide C and vice versa. The two-headed arrow (↔) indicates that A and C replace each other during transcription. One-headed arrows (→) indicate asymmetric exchanges: in the example A → C → G → A, nucleotide A is systematically incorporated in place of every C; similarly, C replaces G and G replaces A during RNA polymerisation. Transcripts corresponding to systematic exchanges are called swinger RNAs. BLASTn analyses detect about 100 predicted swinger RNAs (longer than 100 nucleotides) in GenBank's EST database in addition to the (approximately) 10,000 canonical human mitochondrial RNAs in that database. Hence, about 1% of the human mitochondrial transcripts in GenBank's EST database correspond to 1 among 23 systematic nucleotide exchanges [25–28]. These systematic nucleotide exchanges (an expression that fits chemical contexts) are called bijective transformations in mathematical contexts [29–31]; swinger transcription fits biological contexts.

Mitogenomes are comparatively small, also because of the selection against multiple direct repeats [32–35] and invert repeats [15]: these form secondary structures that are frequently excised; such deletions are frequently deleterious. Vertebrate mitogenomes have densely packed coding and non-coding regions templating for RNAs. Non-canonical transformations greatly increase potential numbers of RNA products for single sequences: four and five RNA transcripts when assuming systematic deletions of mono- and dinucleotides for deltranscriptions, respectively, and 23 swinger RNAs when considering systematic nucleotide exchanges. Therefore, studies of swinger transformations focus on the human mitogenome, which is short (16,569 bp), hence reducing potential false-positive detections due to sheer genome size and because ample sequence data are available from several sources for this organism.

Note that swinger DNA has been detected (mainly corresponding to rRNA genes) for mitochondrial and nuclear sequences [36–38]. Hence, swinger RNAs result from canonical transcription of swinger-transformed DNA or swinger transcription of regular DNA [22]. Some mass spectra match predicted peptides translated from del- and swinger-transformed RNA [39–42]. Detection of chimeric RNAs, consisting of part regular, and part swinger-transformed contiguous sequences suggests that regular canonical and swinger-transformed RNA result from single polymerisation events, probably by the same polymerase [43]. Peptides corresponding to such chimeric RNAs also occur [44].

Secondary structure formation by swinger-transformed sequences associates with swinger RNA detection [45], suggesting regulation of swinger RNA processing by secondary structures, as observed for canonical mitochondrial RNAs, i.e. tRNA punctuation [46].

Abundances of human mitochondrial swinger RNAs detected in GenBank's EST database [25, 26], originating from various sources using Sanger sequencing, are proportional to those detected in transcriptomic data produced by next-generation sequencing, Illumina technology [47]. Similarly, abundances and lengths of swinger RNAs detected in *Mimivirus*' transcriptome sequenced by 454 technology are proportional to those detected when using SOLID sequencing [01]. These analyses confirmed that swinger RNAs are not sequencing artefacts due to specific sequencing technologies, but data sources do not exclude contamination by cytosolic RNA. Here, we compare the previously described human mitochondrial swinger transcriptome [39] from a complete human transcriptome (including cytosolic RNAs) with the swinger transcriptome as detected in purified human mitochondrial lines [48]. Reproducibility of swinger RNA coverages of the human mitogenome would exclude sequencing artefacts and cytosolic contaminations as alternative explanations for hypothetical swinger RNAs. We predict (1) the detection of swinger RNAs from transcriptomic data extracted from purified mitochondrial lines and (2) high similarities between mitogenomic swinger RNA coverages described here and previously [39].
