Frequency and pattern of heteroplasmy in the complete human mitochondrial genome

Abstract

Determining the levels of human mitochondrial heteroplasmy is of utmost importance in several fields. In spite of this, there are currently few published works that have focused on this issue. In order to increase the knowledge of mitochondrial DNA (mtDNA) heteroplasmy, the main goal of this work is to investigate the frequency and the mutational spectrum of heteroplasmy in the human mtDNA genome. To address this, a set of nine primer pairs designed to avoid co-amplification of nuclear DNA (nDNA) sequences of mitochondrial origin (NUMTs) was used to amplify the mitochondrial genome in 101 individuals. The analysed individuals represent a collection with a balanced representation of genders and mtDNA haplogroup distribution, similar to that of a Western European population. The results show that the frequency of heteroplasmic individuals exceeds 61%. The frequency of point heteroplasmy is 28.7%, with a widespread distribution across the entire mtDNA. In addition, an excess of transitions in heteroplasmy were detected, suggesting that genetic drift and/or selection may be acting to reduce its frequency at population level. In fact, heteroplasmy at highly stable positions might have a greater impact on the viability of mitochondria, suggesting that purifying selection must be operating to prevent their fixation within individuals. This study analyses the frequency of heteroplasmy in a healthy population, carrying out an evolutionary analysis of the detected changes and providing a new perspective with important consequences in medical, evolutionary and forensic fields.

Figure 1. Schematic information of point heteroplasmies analysed in the present study and reported by Li et al.

. Information about distribution along the mtDNA genome, kind of mutation (synonymous/non-synonymous), stability^a of positions and implication in secondary and tertiary structure is reported. (PH: point heteroplasmy, S: synonymous, NS: non-synonymous). ^a Defined by: distribution in database population, number of hits in the phylogeny and nucleotide and amino acid conservation index.

Figure 2. Secondary and tertiary structures prediction.

The secondary structure below is coloured by base-pairing probabilities, for unpaired regions the colour denotes the probability of being unpaired. Structure drawing encoding positional entropy is reported in Figure S2. (WT: wild-type, Mut: mutated). (a) Secondary structure prediction of threonine tRNA and implication of point heteroplasmic position 15908. (b) Secondary structure prediction of 12S RNA and implication of point heteroplasmic position 3014. Detailed view of wild-type and mutated position is showed. (c) Three-dimensional model of human COXII complex. Detailed H-bond differences between the wild-type Asp57 and the mutated Asn57 due to a point heteroplasmic position 7754 are presented.