Research Article: Transcripts with systematic nucleotide deletion of 1-12 nucleotide in human mitochondrion suggest potential non-canonical transcription

Date Published: May 23, 2019

Publisher: Public Library of Science

Author(s): Ganesh Warthi, Hervé Seligmann, Thomas Preiss.

http://doi.org/10.1371/journal.pone.0217356

Abstract

Raw transcriptomic data contain numerous RNA reads whose homology with template DNA doesn’t match canonical transcription. Transcriptome analyses usually ignore such noncanonical RNA reads. Here, analyses search for noncanonical mitochondrial RNAs systematically deleting 1 to 12 nucleotides after each transcribed nucleotide triplet, producing deletion-RNAs (delRNAs). We detected delRNAs in the human whole cell and purified mitochondrial transcriptomes, and in Genbank’s human EST database corresponding to systematic deletions of 1 to 12 nucleotides after each transcribed trinucleotide. DelRNAs detected in both transcriptomes mapped along with 55.63% of the EST delRNAs. A bias exists for delRNAs covering identical mitogenomic regions in both transcriptomic and EST datasets. Among 227 delRNAs detected in these 3 datasets, 81.1% and 8.4% of delRNAs were mapped on mitochondrial coding and hypervariable region 2 of dloop. Del-transcription analyses of GenBank’s EST database confirm observations from whole cell and purified mitochondrial transcriptomes, eliminating the possibility that detected delRNAs are false positives matches, cytosolic DNA/RNA nuclear contamination or sequencing artefacts. These detected delRNAs are enriched in frameshift-inducing homopolymers and are poor in frameshift-preventing circular code codons (a set of 20 codons which regulate reading frame detection, over- and underrepresented in coding and other frames of genes, respectively) suggesting a motif-based regulation of non-canonical transcription. These findings show that rare non-canonical transcripts exist. Such non canonical del-transcription does increases mitochondrial coding potential and non-coding regulation of intracellular mechanisms, and could explain the dark DNA conundrum.

Partial Text

Raw transcriptomic data include RNA reads that do not correspond to canonical transcription of the genome [1]. The DNA template of most known noncanonical RNAs is easily recovered because their sequence usually differs from the template DNA by few single nucleotide edits. Around 80–90% of the human genome is transcribed at some point during development [2,3] and has biochemical functions [4]. Most noncanonical transcripts are noncoding RNAs (ncRNAs). Small ncRNAs are <200bp long and contribute to transcription activation [5], transcription maintenance [6], translation inhibition [7], mRNA degradation [8], gene regulation [9], epigenetic modification [10,11], and RNA polymerase II backtracking [9]. Other unknown roles might exist. These coding and non-coding RNAs in the transcriptome were detected assuming canonical transcription, and transcripts not matching template DNA were ignored in further analyses. Hence this genetic information is lost because it is not considered in the analyses of non-canonical transcription. This lost genetic information could possess answers to many questions related to evolution, genetic diseases and could explain dark DNA conundrum. In this study we tested a phenomenon of systematic nucleotide deletion during transcription in three independent datasets. Results confirm the working hypotheses that sometimes, transcription systematically deletes nucleotides. Analyses detect delRNAs corresponding to systematic deletion of 1 to 12 nucleotides after every transcribed tri-nucleotide in the human mitochondrial transcriptome, for three independent transcriptome datasets, two sequenced by NGS methodologies and one by Sanger methodology. Numerous delRNAs were detected in all three datasets, indicating high reproducibility of the human mitochondrial del-transcriptome. DelRNAs detected in this study are around 25–30 bp long. BLASTN search of delRNA3-1 transformed mitogenome aligned with much longer ESTs having a systematic single gap in subject sequence and having continuous alignment at the terminals of the subject sequence (Not shown here). We believe these delRNAs could be part of much longer chimeric RNAs due to the RNA polymerase switching from canonical transcription to non-canonical del-transcription.   Source: http://doi.org/10.1371/journal.pone.0217356

 

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