Transcripts with systematic nucleotide deletion of 1-12 nucleotide in human mitochondrion suggest potential non-canonical transcription.
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 aft...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2019-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0217356 |
| _version_ | 1797635231964987392 |
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| author | Ganesh Warthi Hervé Seligmann |
| author_facet | Ganesh Warthi Hervé Seligmann |
| author_sort | Ganesh Warthi |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-11T12:19:14Z |
| format | Article |
| id | doaj.art-e81fcd480b1949059f4e5649d5d52edb |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-03-11T12:19:14Z |
| publishDate | 2019-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-e81fcd480b1949059f4e5649d5d52edb2023-11-07T05:36:29ZengPublic Library of Science (PLoS)PLoS ONE1932-62032019-01-01145e021735610.1371/journal.pone.0217356Transcripts with systematic nucleotide deletion of 1-12 nucleotide in human mitochondrion suggest potential non-canonical transcription.Ganesh WarthiHervé SeligmannRaw 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.https://doi.org/10.1371/journal.pone.0217356 |
| spellingShingle | Ganesh Warthi Hervé Seligmann Transcripts with systematic nucleotide deletion of 1-12 nucleotide in human mitochondrion suggest potential non-canonical transcription. PLoS ONE |
| title | Transcripts with systematic nucleotide deletion of 1-12 nucleotide in human mitochondrion suggest potential non-canonical transcription. |
| title_full | Transcripts with systematic nucleotide deletion of 1-12 nucleotide in human mitochondrion suggest potential non-canonical transcription. |
| title_fullStr | Transcripts with systematic nucleotide deletion of 1-12 nucleotide in human mitochondrion suggest potential non-canonical transcription. |
| title_full_unstemmed | Transcripts with systematic nucleotide deletion of 1-12 nucleotide in human mitochondrion suggest potential non-canonical transcription. |
| title_short | Transcripts with systematic nucleotide deletion of 1-12 nucleotide in human mitochondrion suggest potential non-canonical transcription. |
| title_sort | transcripts with systematic nucleotide deletion of 1 12 nucleotide in human mitochondrion suggest potential non canonical transcription |
| url | https://doi.org/10.1371/journal.pone.0217356 |
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