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 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.原始转录组数据包含大量RNA读段，其与模板DNA的同源性不符合经典转录特征。常规转录组分析往往会忽略这类非经典RNA读段。本研究针对非经典线粒体RNA展开系统性分析，检索每个转录三核苷酸后删除1至12个核苷酸的序列，由此生成缺失型RNA（deletion-RNAs, delRNAs）。我们在人类全细胞及纯化线粒体转录组中，以及GenBank的人类表达序列标签（Expressed Sequence Tag, EST）数据库内，均检测到了对应于每个转录三核苷酸后系统性删除1~12个核苷酸的delRNAs。在两类转录组中检出的delRNAs，可与55.63%的EST来源delRNAs实现映射匹配。在转录组与EST数据集的delRNAs中，存在覆盖线粒体基因组相同区域的分布偏好性。在这3个数据集中共检出227条delRNAs，其中81.1%与8.4%的delRNAs分别定位于线粒体编码区以及线粒体D环的高变区2。针对GenBank的EST数据库开展的缺失转录分析验证了全细胞及纯化线粒体转录组的观测结果，排除了检出的delRNAs为假阳性匹配、核源性胞质DNA/RNA污染或测序伪影的可能性。这些检出的delRNAs在易引发移码的均聚物中富集，而在可防止移码的环形密码子（一套共20个可调控读框识别的密码子，分别在基因的编码框与其他读框中呈现过表达与低表达特征）中含量匮乏，提示存在基于基序的非经典转录调控机制。上述研究结果证实，罕见的非经典转录本确实存在。这类非经典的缺失转录可增强线粒体编码潜能，并参与胞内生命活动的非编码调控，或可解释暗DNA谜题。