The tRNA genes punctuate the reading of genetic information in human mitochondrial DNA.

A detailed transcription map of HeLa cell mitochondrial DNA (mtDNA) has been constructed by using the S1 protection technique to localize precisely the sequences coding for the ribosomal RNA (rRNA) and poly(A)-containing species on the physical map of the DNA. This transcription map has been correlated with the positions of the tRNA genes derived from the mtDNA sequence. It has been shown that, with the exception of the D loop and another small segment near the origin of replication, the mtDNA sequences are completely saturated by the rRNAs, poly(A)-containing RNAs and tRNA coded for by the two strands. No evidence for intervening sequences has been found. The sequences coding for the individual poly(A)-containing RNA and rRNA species appear to be immediately contiguous on one side, and most frequently on both sides, to tRNA coding sequences. Furthermore, the H strand sequences coding for the two rRNAs, the poly(A)-containing RNAs and the tRNAs appear to be adjacent to each other, extending from coordinate 2/100 to coordinate 95/100 of the genome relative to the origin taken as 0/100. The results are consistent with a model of transcription of the H strand in the form of a single molecule which is processed into mature RNA species by precise endonucleolytic cleavages, occurring in almost all cases immediately before and after a tRNA sequence. The tRNA sequences may play an important role as recognition signals in the processing of the primary transcripts.