| Abstract: | ![]()
Although previous studies have documented a bottleneck in the transmission of mtDNA genomes from mothers to offspring, several aspects remain unclear, including the size and nature of the bottleneck. Here, we analyze the dynamics of mtDNA heteroplasmy transmission in the Genomes of the Netherlands (GoNL) data, which consists of complete mtDNA genome sequences from 228 trios, eight dizygotic (DZ) twin quartets, and 10 monozygotic (MZ) twin quartets. Using a minor allele frequency (MAF) threshold of 2%, we identified 189 heteroplasmies in the trio mothers, of which 59% were transmitted to offspring, and 159 heteroplasmies in the trio offspring, of which 70% were inherited from the mothers. MZ twin pairs exhibited greater similarity in MAF at heteroplasmic sites than DZ twin pairs, suggesting that the heteroplasmy MAF in the oocyte is the major determinant of the heteroplasmy MAF in the offspring. We used a likelihood method to estimate the effective number of mtDNA genomes transmitted to offspring under different bottleneck models; a variable bottleneck size model provided the best fit to the data, with an estimated mean of nine individual mtDNA genomes transmitted. We also found evidence for negative selection during transmission against novel heteroplasmies (in which the minor allele has never been observed in polymorphism data). These novel heteroplasmies are enhanced for tRNA and rRNA genes, and mutations associated with mtDNA diseases frequently occur in these genes. Our results thus suggest that the female germ line is able to recognize and select against deleterious heteroplasmies.Heteroplasmy (intra-individual variation) in mitochondrial DNA (mtDNA) plays an important role in mtDNA-related diseases and has also been implicated in aging and cancer (Greaves et al. 2012; Wallace 2012; Chinnery and Hudson 2013; Lombès et al. 2014). Most mtDNA mutations that cause diseases due to defects in mitochondrial function exist as heteroplasmies and only cause disease symptoms when the frequency of the mutant allele exceeds a particular threshold (Wallace and Chalkia 2013). Below this threshold, individuals are asymptomatic, presumably because there are sufficient functional mitochondria for normal metabolism. Changes in the frequency of pathogenic mutations during the transmission of heteroplasmies from mothers to offspring can thus play an important role in the disease risk of the offspring. However, most of our knowledge concerning the dynamics of heteroplasmy transmission comes from studies of pathogenic mutations (Monnot et al. 2011; Shen et al. 2012; de Laat et al. 2013; Wallace and Chalkia 2013), which in blood have been shown to decrease over time and hence may not accurately reflect the overall level of such pathogenic mutations within an individual (Poulton and Morten 1993; ‘t Hart et al. 1996; Rahman et al. 2001; Rajasimha et al. 2008). Mouse models have also been utilized (Cree et al. 2008; Fan et al. 2008; Freyer et al. 2012; Ross et al. 2013), but to date, there have been only a few studies of normal patterns of heteroplasmy transmission in humans (Sekiguchi et al. 2003; Goto et al. 2011; Sondheimer et al. 2011; Guo et al. 2013; Rebolledo-Jaramillo et al. 2014), including studies of oocytes and placenta (Marchington et al. 1997, 2002; Jacobs et al. 2007), and several questions remain.For example, although it is clear that a bottleneck occurs during the transmission of mtDNA genomes from mothers to offspring, the size of the bottleneck remains a contentious issue. Previous estimates of the effective number of transmitted mtDNA genomes range widely, from eight to 200 (Brown et al. 2001; Guo et al. 2013; Rebolledo-Jaramillo et al. 2014). However, all previous studies have assumed a constant size for the bottleneck across individuals; the effect of allowing the bottleneck size to vary among individuals has not been investigated. Moreover, it has been suggested that mtDNA genomes may not behave as independent entities but instead are organized into discrete units called “nucleoids,” each of which contains 5–10 mtDNA genomes (Jacobs et al. 2000; Cao et al. 2007; Khrapko 2008), although recently it has been suggested that the number may be much smaller, on the order of one mtDNA genome per nucleoid (Kukat et al. 2011). Each nucleoid is thought to be homoplasmic for mtDNA genome sequences; thus, mtDNA heteroplasmy at the cellular level would reflect nucleoids that are homoplasmic for different sequence variants. Nucleoid structures within cells have been studied microscopically and biochemically (Bogenhagen 2012), and nucleoid-based models have been found to provide a better fit to the segregation of heteroplasmic mtDNA genomes in cell lines than do simple bottleneck models in some studies (Cao et al. 2007; Khrapko 2008), but not in others (Cree et al. 2008). However, to date, nucleoid-based models have not been investigated in the transmission of mtDNA heteroplasmy from mothers to offspring.Another issue is the degree to which negative (or purifying) selection may act on deleterious variants during the transmission of mtDNA heteroplasmy. There are conflicting results and views as to whether changes in the frequency of a heteroplasmic mutation from mother to offspring are governed solely by genetic drift, or whether there is an additional role for negative (purifying) selection (Jenuth et al. 1997; Durham et al. 2006; Stewart et al. 2008a,b; Wonnapinij et al. 2008; Wallace and Chalkia 2013; Rebolledo-Jaramillo et al. 2014). Negative selection during heteroplasmy transmission, as evidenced by a decrease in the frequency of presumably deleterious heteroplasmic variants in offspring compared to mothers, must operate on the female germ line and/or early in development after fertilization, and hence differs from negative selection operating on homoplasmic variants that reduce viability or fertility (Holt et al. 2014). The opportunities for, and extent of, such negative selection during heteroplasmy transmission in humans remain largely unknown.Here, we utilize the Genomes of the Netherlands (GoNL) project (Boomsma et al. 2014; Genome of the Netherlands Consortium 2014), consisting of whole-genome sequence data from blood samples from 250 families, to carry out the largest study to date (to our knowledge) of the dynamics of heteroplasmy transmission across the entire mtDNA genome. We utilize the data on changes in minor allele frequency (MAF) from mothers to offspring at heteroplasmic sites to compare different models for the inheritance of mtDNA genomes, and we analyze the data for evidence of negative selection during heteroplasmy transmission. |
