Analysis of phylogenetically reconstructed mutational spectra in human mitochondrial DNA control region

Abstract

Analysis of mutations in mitochondrial DNA is an important issue in population and evolutionary genetics. To study spontaneous base substitutions in human mitochondrial DNA we reconstructed the mutational spectra of the hypervariable segments I and II (HVS I and II) using published data on polymorphisms from various human populations. An excess of pyrimidine transitions was found both in HVS I and II regions. By means of classification analysis numerous mutational hotspots were revealed in these spectra. Context analysis of hotspots revealed a complex influence of neighboring bases on mutagenesis in the HVS I region. Further statistical analysis suggested that a transient misalignment dislocation mutagenesis operating in monotonous runs of nucleotides play an important role for generating base substitutions in mitochondrial DNA and define context properties of mtDNA. Our results suggest that dislocation mutagenesis in HVS I and II is a fingerprint of errors produced by DNA polymerase gamma in the course of human mitochondrial DNA replication

Site-specific somatic mitochondrial DNA point mutations in patients with thymidine phosphorylase deficiency

“…In this situation, the T·T mispair is formed -not by direct misincorporation, but by the transient misalignment -and leads to a Tto-A transversion as observed in the in vitro mtDNA pol γ medication assay (29) (Figure 1). Of note, an analysis of published HVS 1 and HVS 2 polymorphisms in various human populations suggested that dislocation mutagenesis contributes to the generation of base substitutions, particularly in monotonous runs of nucleotides (15). In contrast to our observations in MNGIE patients, previous studies of mutations produced by mtDNA pol γ in vitro have not revealed enhanced point mutations in short homopolymeric runs; however, these studies have used balanced nucleotide pools (29).…”

“…To screen for mutations at non-5′-AAAT sites, we sequenced HVS 1 and HVS 2 in the mtDNA D-loop, which are considered to be hot spots for mutations (13)(14)(15). We subcloned PCRamplified HVSs of cultured skin fibroblast mtDNA from two patients (MN4-3 and MN7-1) and two controls, and sequenced between 84 and 92 clones of each PCR fragment.…”

“…The existence of hypervariable segments (HVSs) in the noncoding human mtDNA control region has been well documented in numerous analyses of human mtDNA variation, and HVS 1 and HVS 2 are thought to be mutational hot spots (13)(14)(15). To screen HVS 1 and HVS 2, fragments spanning nucleotides 15,975 to 635 (16) were amplified by PCR from purified DNA samples using a forward primer (nucleotides 15,975-15,994), a backward primer (nucleotides 635-616), and Platinum Taq DNA Polymerase High Fidelity (Invitrogen Corp.).…”

Mitochondrial DNA sequence variation in single cells from leukemia patients

“…Among them, mutations 146, 185, 204, and 16189 have been scored as mutation hot spots in human mtDNA control region that was based on population data. 23,24,37,38 It thus seems that somatic mutation events in single hematopoietic cells are also prone to occur at well-characterized mutational hot spots, as has been observed in patients with primary tumors of the central nervous system. 33 Our observed mtDNA mutation spectrum of single cells from the normal and leukemic hematopoietic system also differs from the patterns that were described in aging tissues, [39][40][41] Alzheimer disease brain, 42 cardiomyocytes, 43 and neurons and glia, 44 suggesting tissue specificity and adding further complexity to our view of the mutation process in leukemia.…”

mtDNA mutations in tumors of the central nervous system reflect the neutral evolution of mtDNA in populations

“…Within the group of hotspots are positions 16 189 in HVS-I, as well as 146, 150, 152, and 185 in HVS-II, all of them found to harbor mutations in our CNS tumor samples. These positions are at or near the top of the lists of hotspots recently constructed by Malyarchuk et al (2002) and Bandelt et al (2002), the only exception being position 16 069, which cannot be regarded as a hotspot; it may evolve at about the average rate for HVS-I (Meyer et al, 1999).…”