Precise annotation of human, chimpanzee, rhesus macaque and mouse mitochondrial genomes leads to insight into mitochondrial transcription in mammals

• Published in: RNA biology 2020-03, Vol.17 (3), p.395-402
• Main Authors: Jin, Xiufeng, Cheng, Zhi, Wang, Bo, Yau, Tung on, Chen, Ze, Barker, Stephen C., Chen, Defu, Bu, Wenjun, Sun, Daqing, Gao, Shan
• Format: Article
• Language: English
• Subjects: Animals; Base Sequence; Conserved Sequence; control region; Genes, Mitochondrial; Genome, Human; Genome, Mitochondrial; Humans; Macaca mulatta - genetics; Mammals - genetics; Mice; Mitochondrial DNA; mitochondrial transcription; Molecular Sequence Annotation; Pan troglodytes - genetics; precise annotation; Research Paper; RNA, Antisense; Transcription Initiation Site; Transcription, Genetic; uninterrupted transcription
• ISSN: 1547-6286; 1555-8584
• DOI: 10.1080/15476286.2019.1709746

In the present study, we applied our 'precise annotation' to the mitochondrial (mt) genomes of human, chimpanzee, rhesus macaque and mouse using 5′ and 3′ end small RNAs. Our new annotations updated previous annotations. In particular, our new annotations led to two important novel findings: (1) the identification of five Conserved Sequence Blocks (CSB1, CSB2, CSB3, LSP and HSP) in the control regions; and (2) the annotation of Transcription Initiation and novel Transcription Termination Sites. Based on these annotations, we proposed a novel model of mt transcription which can account for the mt transcription and its regulation in mammals. According to our model, Transcription Termination Sites function as switches to regulate the production of short, long primary transcripts and uninterrupted transcription, rather than simply terminate the mt transcription. Moreover, the expression levels of mitochondrial transcription termination factors control the proportions of rRNAs, mRNAs and lncRNAs in total mt RNA. Our findings point to the existence of many other, as yet unidentified, Transcription Termination Sites in mammals.