Effect of length variations at nucleotide positions 303-315 in human mitochondrial DNA on transcription termination

In addition to stabilizing the RNA-DNA hybrid, conserved sequence block (CSB) II, which is located at nucleotides 299-315 on mitochondrial DNA, relates with the transcription termination for initiation of heavy strand synthesis in human mitochondrial replication. Due to length polymorphisms at nucleotides 303-315, individuals contain homo- or heteroplasmic profiles with length variants from C5TC6 to C15TC6 or from C9 to C13. Using in vitro transcription with templates containing these variations, we demonstrated that the production of prematurely terminated (PT) transcripts depends on the 303-315 sequences, and that longer templates result in relatively higher levels of PT transcripts. The 3′ ends of PT transcripts were observed within or downstream of CSB II. Termination positions downstream of nucleotide 303 were shifted upstream by longer variations, but not shifted by shorter variations. We found that length variations between 303 and 315 generate quantitative and qualitative differences in PT transcripts.