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Infertility affects one in six couples, half of which are caused by a male factor. Male infertility can be caused by both, qualitative and quantitative defects, leading to Oligo- astheno-terato-zoospermia (OAT; impairment in ejaculate sperm cell concentration, motility and morphology). Azoospermia defined as complete absence of sperm cells in the ejaculation. While hundreds of genes are involved in spermatogenesis the genetic etiology of men's infertility remains incomplete.We identified a hemizygous stop gain pathogenic variation (PV) in the X-linked Germ Cell Nuclear Acidic Peptidase (GCNA), in an Azoospermic patient by exome sequencing. Assessment of the prevalence of pathogenic variations in this gene in infertile males by exome sequence data of 11 additional unrelated patients identified a probable hemizygous causative missense PV in GCNA in a severe OAT patient. Expression of GCNA in the patients' testes biopsies and the stage of spermatogonial developmental arrest were determined by immunofluorescence and immunohistochemistry. The Azoospermic patient presented spermatogenic maturation arrest with an almost complete absence of early and late primary spermatocytes and thus the complete absence of sperm. GCNA is critical for genome integrity and its loss results in genomic instability and infertility in Drosophila, C. elegans, zebrafish, and mouse. PVs in GCNA appear to be incompatible with male fertility in humans as well: A stop-gain PV caused Azoospermia and a missense PV caused severe OAT with very low fertilization rates and no pregnancy in numerous IVF treatments.

Species living in a changing environment are capable of adapting to alterations of various factors. Physiological acclimatization may be significantly influenced by the heterozygosity, especially with regards to allele variance and its specific expression (ASE) under different conditions. Data from RNA-seq experiments can be used to identify and quantify the alleles expressed, in order to detect and characterize ASE and regulation of gene expression. However, the allele matching the reference genome creates a mapping bias that prevents a reliable estimation of the allele depth unless the haplotype of the experimental individuals is provided. We developed a pipeline that allows the identification of the alleles corresponding to an RNA-seq dataset and their unbiased quantification. This pipeline does not require the sequencing of the DNA nor the previous knowledge of the haplotype. The identified SNPs are further substituted in the reference genome, thus creating two pseudogenomes with the alternative alleles on two independent samples of the experiment. The SNPs are further called against each pseudogenome thus providing with two SNP datasets that are averaged for calculation of the allele depth. The final SNP calling file contains the coordinates of the SNPs and also the ID of genes containing the SNPs, the expressed genotypes, the unbiased allele depth and the statistical tests for identifying ASE according to the experimental design and correlated with differentially expressed genes. Therefore, the pipeline presented here can calculate ASE in non-model organisms and can be applied to previous RNA-seq datasets for expanding studies in gene expression regulation.

The objectives were to estimate the effects of various environmental factors on female calf survival of Israeli Holsteins, to estimate the economic value of calf survival under Israeli conditions, to estimate the genetic and environmental variance components for calf and cow survival using the individual animal model, to perform GWAS analyses of survival to first calving and herd life after first calving, to estimate the genetic and environmental trends for calf survival since 1985, to estimate genetic correlations of calf survival with the traits included in the current Israeli breeding index, and to estimate the consequences of inclusion of calf survival in the national selection index. Mean calf survival rate of Israeli Holsteins from 2001 through 2008 was 0.85, and the mean economic value of survival to first calving was $526. Birth month, gestation length, dystocia, and twin birth significantly affected calf survival rate. Dystocia and twin birth each reduced survival rate by 0.034. Survival rate was highest for calves born in October and lowest for calves born in February. The difference between these months was 3.4%. Maximum survival was at a gestation length of 276 d, the mean gestation length for this population. Survival rate was reduced to 0.76 for calves born after a gestation length of 260 d. The individual animal model was applied for all the genetic analyses. Heritability for calf survival to first calving, as estimated by REML, was 0.009, whereas heritability of herd life from first calving was 0.15. The complete data set for genetic analysis of survival to first calving included 1,235,815 calves born between 1985 and 2017. Annual genetic and phenotypic trends for calf survival were 0.019 and 0.015%, respectively. Correlations of transmitting abilities of 226 sires born since 2010 for calf survival with the traits included in the Israeli breeding index were significant only for the maternal effects of dystocia and stillbirth. The GWAS analysis was based on the transmitting abilities of 1,493 bulls with genotypes and reliabilities >0.5 for calf survival and cow herd life. There were 7 single nucleotide polymorphisms with coefficients of determination >0.03 for calf survival and 12 single nucleotide polymorphisms with coefficients of determination >0.05 for cow survival. There was no overlap between the genome-wide significant markers for the GWAS analyses of calf survival and cow herd life. This corresponds to the conclusion from the REML results and the low correlations between the sire evaluations that the genetic control of the 2 traits are not similar. Inclusion of calf survival in the Israeli breeding would result in a 0.5% increase in calf survival over 10 yr but reduce progress for the other traits by 8%.

BackgroundOligoteratoasthenozoospermia (OTA) combines deteriorated quantity, morphology and motility of the sperm, resulting in male factor infertility.MethodsWe used whole genome genotyping and exome sequencing to identify the mutation causing OTA in four men in a consanguineous Bedouin family. We expressed the normal and mutated proteins tagged with c-Myc at the carboxy termini by transfection with pCDNA3.1 plasmid constructs to evaluate the effects on protein stability in HEK293 cells and on the kinetics of actin repolymerisation in retinal pigment epithelium cells. Patients’ sperm samples were visualised by transmission electron microscopy to determine axoneme structures and were stained with fluorescent phalloidin to visualise the fibrillar (F)-actin.ResultsA homozygous missense mutation in Ciliogenesis Associated TTC17 Interacting Protein (CATIP): c. T103A, p. Phe35Ile, a gene encoding a protein important in actin organisation and ciliogenesis, was identified as the causative mutation with a LOD score of 3.25. The mutation reduces the protein stability compared with the normal protein. Furthermore, overexpression of the normal protein, but not the mutated protein, inhibits repolymerisation of actin after disruption with cytochalasin D. A high percentage of spermatozoa axonemes from patients have abnormalities, as well as disturbances in the distribution of F-actin.ConclusionThis is the first report of a recessive mutation in CATIP in humans. The identified mutation may contribute to asthenozoospermia by its involvement in actin polymerisation and on the actin cytoskeleton. A mouse knockout homozygote for CATIP was reported to demonstrate male infertility as the sole phenotype.

One of the causes of observed low fertility is embryo loss after fertilization. Previous findings suggested that more than half of fertilizations result in embryo loss before pregnancy is detected. We proposed reinsemination between 49 and 100 d after the first insemination as an indicator trait for early abortion (EA) in dairy cattle based on the mean estrus interval of 21 d. This trait was compared with conception rate from first insemination and conception status, computed as the inverse of the number of inseminations to conception. Animal model variance components were estimated by REML, including parents and grandparents of cows with records. First-parity heritability for first insemination conception rate was 3%. In the multitrait analysis of parities 1 to 3 for putative EA, heritabilities ranged from 8.9% for first parity to 10.4% for second parity. All genetic correlations were0.9, whereas all environmental correlations were0.12. The variance component for the service sire effect for putative EA rate was less than half the variance component for conception rate. Thus, genetic control of the 2 traits is clearly different, and analysis of EA rate by a single-trait animal model is justified. Genetic evaluation for putative EA was computed using this model, including all first- through third-parity cows with freshening dates from January 1, 1985, through December 31, 2016, that either became pregnant on first insemination or were reinseminated between 49 and 100 d after the first insemination. All known parents and grandparents of cows with records were included in the analysis. The regression of the breeding value for non-abortion rate on the cows' birth year was 0.083%/yr. The genetic correlation between first-parity EA and conception status was 0.995. The genetic correlations between first-parity EA and milk, fat, and protein production were all negative, whereas the genetic correlation between EA and herd life was 0.33. Inclusion of putative EA in the selection index instead of conception status resulted in 10 to 20% greater genetic gain for both fertility traits. In a genome-wide association study based on 1,200 dairy bulls with reliabilities50% for abortion rate genotyped for 41,000 markers, 6 markers were found with nominal probabilities of10

Macroautophagy/autophagy is a conserved catabolic process that maintains cellular homeostasis under basal growth and stress conditions. In cancer, autophagy can either prevent or promote tumor growth, at early or advanced stages, respectively. We screened public databases to identify autophagy-related somatic mutations in cancer, using a computational approach to identify cancer mutational target sites, employing exact statistics. The top significant hit was a missense mutation (Y113C) in the MAP1LC3B/LC3B (microtubule associated protein 1 light chain 3 beta) protein, which occurred at a significant frequency in cancer, and was detected in early stages in primary tumors of patients with known tumor lineage. The mutation reduced the formation of GFP-LC3B puncta and attenuated LC3B lipidation during Torin1-induced autophagy. Its effect on the direct physical interaction of LC3B with each of the 4 proteins that control its maturation or lipidation was tested by applying a protein-fragment complementation assay and co-immunoprecipitation experiments. Interactions with ATG4A and ATG4B proteases were reduced, yet without perturbing the cleavage of mutant LC3B. Most importantly, the mutation significantly reduced the interaction with the E1-like enzyme ATG7, but not the direct interaction with the E2-like enzyme ATG3, suggesting a selective perturbation in the binding of LC3B to some of its partner proteins. Structure analysis and molecular dynamics simulations of LC3B protein and its mutant suggest that the mutation changes the conformation of a loop that has several contact sites with ATG4B and the ATG7 homodimer. We suggest that this loss-of-function mutation, which attenuates autophagy, may promote early stages of cancer development.

Transposon insertion sequencing is a powerful tool, but many researchers are discouraged by the apparent technical complexity of preparing the genomic library for deep sequencing and by the complicated computational analysis needed for insertion site identification. Our proposed method makes the preparation of the library easy and straightforward, relying on well-known molecular biology techniques. In addition, the results obtained from the deep sequencing are easily analyzed in terms of transposon insertion site identification, placing library preparation and analysis within the reach of more researchers in the microbiology community, including those with less computational and bioinformatic resources and experience. This is demonstrated by analysis of the most saturated Tn-mutant library created to date in the emerging pathogen Mycobacterium abscessus., We present a technically simple, easy-to-perform method for generating the genomic libraries for Himar-1 transposon site sequencing (Tn-seq). In addition to being simpler than present methods in the technical aspect, it also allows more robust and straightforward identification of the insertion site, by generating a longer sequence surrounding the insertion TA in the genome. The method makes Tn-seq more user-friendly and accessible to laboratories with more-limited bioinformatic resources. Finally, we created a saturated transposon-mutant library in Mycobacterium abscessus and demonstrated the usefulness of the method in analysis of genes involved in colony morphology, as well as in analysis of the whole Tn-mutant library, with identification of over 8,000 unique mutants. IMPORTANCE Transposon insertion sequencing is a powerful tool, but many researchers are discouraged by the apparent technical complexity of preparing the genomic library for deep sequencing and by the complicated computational analysis needed for insertion site identification. Our proposed method makes the preparation of the library easy and straightforward, relying on well-known molecular biology techniques. In addition, the results obtained from the deep sequencing are easily analyzed in terms of transposon insertion site identification, placing library preparation and analysis within the reach of more researchers in the microbiology community, including those with less computational and bioinformatic resources and experience. This is demonstrated by analysis of the most saturated Tn-mutant library created to date in the emerging pathogen Mycobacterium abscessus.

Age and sex were shown to affect the prevalence and the manifestation of many respiratory infectious diseases. These can be attributed to age and sex related alterations in the immune system and in the lung functions. Since the outbreak of COVID-19, epidemiological studies consistently report that age and sex are major risk factors in both morbidity and mortality due to COVID-19. Thus, understanding age and sex dependent gene expression in the lung and in the immune system can provide mechanical evidences with respects to sex related higher risk of elderly to develop severe complications in respiratory infectious diseases. In this context, sex- and age- transcriptome analysis from hundreds of lung and blood samples, revealed significant downregulation of the lung surfactant and blood innate immune genes, that occur predominantly in elderly men. Depletion in lung surfactant leads to enhanced injury of alveolar epithelium and fibrotic destruction, and recruitment of the innate immune system is essential to control infection of new pathogens like SARS-CoV-2. Interestingly, surfactant proteins, which protect the lung from infection, are co-produced with the SARS-CoV-2 host receptor- ACE2, by the AT2 cells. Thus, infection by SARS-CoV-2 is expected to lead to decline in AT2 cells and a loss of surfactant proteins, especially in elderly men.

Oligoteratoasthenozoospermia (OTA) combines deteriorated quantity, morphology and motility of the sperm, resulting in male factor infertility.We used whole genome genotyping and exome sequencing to identify the mutation causing OTA in four men in a consanguineous Bedouin family. We expressed the normal and mutated proteins tagged with c-Myc at the carboxy termini by transfection with pCDNA3.1 plasmid constructs to evaluate the effects on protein stability in HEK293 cells and on the kinetics of actin repolymerisation in retinal pigment epithelium cells. Patients' sperm samples were visualised by transmission electron microscopy to determine axoneme structures and were stained with fluorescent phalloidin to visualise the fibrillar (F)-actin.A homozygous missense mutation in Ciliogenesis Associated TTC17 Interacting Protein (This is the first report of a recessive mutation in

Up to 1% of all men experience azoospermia, a condition of complete absence of sperm in the semen. The mechanisms and genes involved in spermatogenesis are mainly studied in model organisms, and their relevance to humans is unclear because human genetic studies are very scarce. Our objective was to uncover novel human mutations and genes causing azoospermia due to testicular meiotic maturation arrest. Affected and unaffected siblings from three families were subjected to whole-exome or whole-genome sequencing, followed by comprehensive bioinformatics analyses to identify mutations suspected to cause azoospermia. These likely mutations were further screened in azoospermic and normozoospermic men and in men proven to be fertile, as well as in a reference database of local populations. We identified three novel likely causative mutations of azoospermia in three genes: MEIOB, TEX14, and DNAH6. These genes are associated with different meiotic processes: meiotic crossovers, daughter cell abscission, and possibly rapid prophase movements. The genes and pathways we identified are fundamental for delineating common causes of azoospermia originating in mutations affecting diverse meiotic processes and have great potential for accelerating approaches to diagnose, treat, and prevent infertility. Genet Med advance online publication 16 February 2017

The MalaCards human disease database (http://www.malacards.org/) is an integrated compendium of annotated diseases mined from 68 data sources. MalaCards has a web card for each of ∼20 000 disease entries, in six global categories. It portrays a broad array of annotation topics in 15 sections, including Summaries, Symptoms, Anatomical Context, Drugs, Genetic Tests, Variations and Publications. The Aliases and Classifications section reflects an algorithm for disease name integration across often-conflicting sources, providing effective annotation consolidation. A central feature is a balanced Genes section, with scores reflecting the strength of disease-gene associations. This is accompanied by other gene-related disease information such as pathways, mouse phenotypes and GO-terms, stemming from MalaCards' affiliation with the GeneCards Suite of databases. MalaCards' capacity to inter-link information from complementary sources, along with its elaborate search function, relational database infrastructure and convenient data dumps, allows it to tackle its rich disease annotation landscape, and facilitates systems analyses and genome sequence interpretation. MalaCards adopts a 'flat' disease-card approach, but each card is mapped to popular hierarchical ontologies (e.g. International Classification of Diseases, Human Phenotype Ontology and Unified Medical Language System) and also contains information about multi-level relations among diseases, thereby providing an optimal tool for disease representation and scrutiny.

Background Crossover localization during meiotic recombination is mediated by the fast-evolving zinc-finger (ZnF) domain of gene PRDM9. To study its impact on dairy cattle performance, we compared its genetic variation between the relatively small Israeli (IL) Holsteins and the North American (US) Holsteins that count millions. Results Initially, we analyzed the major BTA1 haplotypes present in IL Holsteins based on the 10 most telomeric SNPs of the BovineSNP50 BeadChip. Sequencing of representative haplotype carriers indicated that for all frequent haplotypes (> 6%), the variable PRDM9 ZnF array consisted of seven tandem ZnF repeats. Two rare haplotypes (frequency

Female infertility accounts for at least 50% of all human infertility cases. One of the causes contributing for female infertility is embryo loss after fertilization. Previous findings suggested that more than half of fertilizations results in embryo loss before pregnancy is detected. Dairy cattle may be a useful model for study of the genetic architecture of this trait. In advanced commercial populations, all breeding is by artificial insemination, and extensive records of the cows’ estrus, insemination and pregnancies are available. We proposed re-insemination between 49 and 100 days after the first insemination as an indicator trait for early abortion in dairy cattle, based on the mean estrus interval of 21 days. Israeli Holstein cows scored as early abortion were compare to cows recorded as pregnant from the first insemination. This trait was compare to conception rate from first insemination. Animal model variance components were estimated by REML, including parents and grandparents of cows with records. First parity heritability for conception rate was 3%. In the multi-trait analysis of parities 1-3 for abortion rate heritabilities ranged from 8.9% for first parity to 10.4% for second parity. The variance component for the service sire effect for abortion rate were less than half the variance component for conception rate. Thus genetic control of the two traits is clearly different. Genome wide association study were performed based on the genetic evaluations of ∼1200 sires with reliabilities >50%. The markers with the lowest probabilities for early abortion were also included among the markers with the lowest probabilities for conception rate, but not vice versa. The marker explaining the most variance for abortion rate is located within the ABCA9 gene, which is found within an ABC genes cluster. The ATP-binding cassette family is the major class of primary active transporters in the placenta.Author summaryApproximately 70% of human conceptions fail to achieve viability. Almost 50% of all pregnancies end in miscarriage before the clinical recognition of a missed period. Cattle are a useful model for human female reproductive processes, because of the similarities in the reproductive cycles, and the extensive documentation in commercial cattle populations, including estrus and insemination records. In addition to the expected benefits from cow fertility research for human biomedical applications, fertility is an economically important trait in dairy cattle with very low heritability. The mean estrous interval for cattle is 21 days. We therefore proposed re-insemination between 49 and 100 days after the first insemination as an indicator trait for early abortion. Israeli Holstein cows scored as having early abortion based on first insemination after parturition were compare to cows recorded as pregnant from the first insemination. Heritability for early abortion rate was three-fold the heritability for conception rate. In a genome wide association study based on 1200 dairy bulls genotyped for 41,000 markers, six markers were found with nominal probabilities of < 10-12 to reject the null hypothesis of no effect on early abortion rate. Early abortion rate may be a useful indicator trait for improvement of fertility in dairy cattle.

Study question Are there genetic variants that can be used for the clinical evaluation of azoospermic men? Summary answer A novel homozygous frame-shift mutation in the MEIOB gene was identified in three azoospermic patients from two different families. What is known already Up to 1% of all men have complete absence of sperm in the semen, a condition known as azoospermia. There are very few tools for determining the etiology of azoospermia and the likelihood of sperm cells in the testis. The MEIOB gene codes for a single-strand DNA binding protein required for DNA double-strand breaks repair during meiosis. MEIOB appears to be exclusively expressed in human and mouse testis, and MeioB knockout mice are azoospermic due to meiotic arrest. Study design, size, duration Two brothers with non-obstructive azoospermia (NOA) underwent whole-exome sequencing followed by comprehensive bioinformatics analyses. Candidate variations were further screened in infertile and fertile men, as well as in public and local reference databases. Participants/materials, setting, methods This study included 159 infertile and 77 fertile men. The exomes of two Arab men were completely sequenced. In addition, 213 other men of the same Arab ethnicity (136 infertile and 77 fertile men) underwent restriction fragment length polymorphism (RFLP) screening, as did 21 NOA men, of other ethnicities, with testicular impairment of spermatocyte arrest. All of the infertile men underwent Y-chromosome microdeletion and CFTR gene mutation assessments. Comprehensive bioinformatics analyses were designed to uncover candidate mutations associated with azoospermia. Main results and the role of chance A novel homozygous frame-shift mutation in the MEIOB gene was identified in two brothers of Arab ethnicity. This frame-shift is predicted to result in a truncated MEIOB protein, which lacks the conserved C-terminal DNA binding domain. RFLP screening of the mutation in 157 infertile men, including 112 NOA patients of Arab ethnicity, identified an additional unrelated NOA patient with the same homozygous mutation and a similar testicular impairment. This mutation was not found in available public databases (n > 160 000), nor in the 77 proven fertile men, nor in our database of local Israeli population variations derived from exome and genome sequencing data (n = 500). Limitations, reasons for caution We have thus far screened for only two specific MEIOB probable pathogenic mutations in a relatively small local cohort. Therefore, the relative incidence of MEIOB mutations in azoospermia should be further assessed in larger and diverse cohorts in order to determine the efficiency of MEIOB sequence screening for clinical evaluations. Wider implications of the findings The relatively high incidence of likely NOA-causing mutations in MEIOB that was found in our cohort supports the idea that a complete screening of this gene might be beneficial for clinical evaluation of NOA patients. Study funding/competing interest(s) This research was supported in part by a grant to EA from the European Research Council under the European Union's Seventh Framework Programme (FP/2007-2013)/ERC grant agreement (616088). There are no competing interests. Trial registration number N/A.

Objective: To identify the underlying genetic defect in 5 patients from a consanguineous family with a Walker-Warburg phenotype, together with intracranial calcifications. Methods: Homozygosity mapping and exome sequencing, followed by Sanger sequencing of the obtained candidate gene, was performed. Expression of the candidate gene was tested by reverse transcription PCR. Patient fibroblasts were converted to myotubes, and the expression and function of dystroglycan was tested by Western blotting. Results: We detected a homozygous loss-of-function frameshift mutation in the DAG1 gene and showed that this mutation results in a complete absence of both α- and β-dystroglycan. Conclusions: A loss-of-function mutation in DAG1 can result in Walker-Warburg syndrome and is not embryonic lethal.

Background The prevalence of several human morbid phenotypes is sometimes much higher than intuitively expected. This can directly arise from the presence of two sexes, male and female, in one species. Men and women have almost identical genomes but are distinctly dimorphic, with dissimilar disease susceptibilities. Sexually dimorphic traits mainly result from differential expression of genes present in both sexes. Such genes can be subject to different, and even opposing, selection constraints in the two sexes. This can impact human evolution by differential selection on mutations with dissimilar effects on the two sexes. Results We comprehensively mapped human sex-differential genetic architecture across 53 tissues. Analyzing available RNA-sequencing data from 544 adults revealed thousands of genes differentially expressed in the reproductive tracts and tissues common to both sexes. Sex-differential genes are related to various biological systems, and suggest new insights into the pathophysiology of diverse human diseases. We also identified a significant association between sex-specific gene transcription and reduced selection efficiency and accumulation of deleterious mutations, which might affect the prevalence of different traits and diseases. Interestingly, many of the sex-specific genes that also undergo reduced selection efficiency are essential for successful reproduction in men or women. This seeming paradox might partially explain the high incidence of human infertility. Conclusions This work provides a comprehensive overview of the sex-differential transcriptome and its importance to human evolution and human physiology in health and in disease. Electronic supplementary material The online version of this article (doi:10.1186/s12915-017-0352-z) contains supplementary material, which is available to authorized users.

Despite years of research, the structure of the largest mammalian oxidative phosphorylation (OXPHOS) complex, NADH-ubiquinone oxidoreductase (complex I), and the interactions among its 45 subunits are not fully understood. Since complex I harbors subunits encoded by mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) genomes, with the former evolving ∼10 times faster than the latter, tight cytonuclear coevolution is expected and observed. Recently, we identified three nDNA-encoded complex I subunits that underwent accelerated amino acid replacement, suggesting their adjustment to the elevated mtDNA rate of change. Hence, they constitute excellent candidates for binding mtDNA-encoded subunits. Here, we further disentangle the network of physical cytonuclear interactions within complex I by analyzing subunits coevolution. Firstly, relying on the bioinformatic analysis of 10 protein complexes possessing solved structures, we show that signals of coevolution identified physically interacting subunits with nearly 90% accuracy, thus lending support to our approach. When applying this approach to cytonuclear interaction within complex I, we predict that the 'rate-accelerated' nDNA-encoded subunits of complex I, NDUFC2 and NDUFA1, likely interact with the mtDNA-encoded subunits ND5/ND4 and ND5/ND4/ND1, respectively. Furthermore, we predicted interactions among mtDNA-encoded complex I subunits. Using the yeast two-hybrid system, we experimentally confirmed the predicted interactions of human NDUFC2 with ND4, the interactions of human NDUFA1 with ND1 and ND4, and the lack of interaction of NDUFC2 with ND3 and NDUFA1, thus providing a proof of concept for our approach. Our study shows, for the first time, evidence for direct interactions between nDNA-encoded and mtDNA-encoded subunits of human OXPHOS complex I and paves the path towards deciphering subunit interactions within complexes lacking three-dimensional structures. Our subunit-interactions-predicting method, ComplexCorr, is available at http://webclu.bio.wzw.tum.de/complexcorr.

The mutation rate of the mitochondrial DNA (mtDNA), which is higher by an order of magnitude as compared with the nuclear genome, enforces tight mitonuclear coevolution to maintain mitochondrial activities. Interruption of such coevolution plays a role in interpopulation hybrid breakdown, speciation events, and disease susceptibility. Previously, we found an elevated amino acid replacement rate and positive selection in the nuclear DNA-encoded oxidative phosphorylation (OXPHOS) complex I subunit NDUFC2, a phenomenon important for the direct interaction of NDUFC2 with the mtDNA-encoded complex I subunit ND4. This finding underlines the importance of mitonuclear coevolution to physical interactions between mtDNA and nuclear DNA-encoded factors. Nevertheless, it remains unclear whether this interaction is important for the stability and activity of complex I. Here, we show that siRNA silencing of NDUFC2 reduced growth of human D-407 retinal pigment epithelial cells, significantly diminished mitochondrial membrane potential, and interfered with complex I integrity. Moreover, site-directed mutagenesis of a positively selected amino acid in NDUFC2 significantly interfered with the interaction of NDUFC2 with its mtDNA-encoded partner ND4. Finally, we show that a genotype combination involving this amino acid (NDUFC2 residue 46) and the mtDNA haplogroup HV likely altered susceptibility to type 2 diabetes mellitus in Ashkenazi Jews. Therefore, mitonuclear coevolution is important for maintaining mitonuclear factor interactions, OXPHOS, and for human health.

Sex-limited selection can moderate the elimination of deleterious mutations from the population and contribute to the high prevalence of common human diseases. Accordingly, deleterious mutations in autosomal genes that are exclusively expressed in only one of the sexes undergo sex-limited selection and can reach higher frequencies than mutations similarly selected in both sexes. Here we show that the number of deleterious SNPs in genes exclusively expressed in men is twofold higher than in genes that are selected in both sexes. Additional analyses suggest that the increased number of damaging mutations we found in male-specific genes is due to reduced selection in females. These results are noteworthy since many of these male-specific genes are known to be crucial for male reproduction, and are thus likely to be under strong purifying selection. We suggest that inheritance of male-infertility-causative mutations through unaffected female lineages contributes to the high incidence of male infertility.