Dan Mishmar

Ben-Gurion University of the Negev | bgu · Department of Life Sciences

Mitochondrial DNA (mtDNA) harbors essential genes in most metazoans, yet the regulatory impact of the multiple evolutionary mtDNA rearrangements has been overlooked. Here, by analyzing mtDNAs from ~8000 metazoans we found high gene content conservation (especially of protein and rRNA genes), and codon preferences for mtDNA-encoded tRNAs across most...

Mitochondrial dysfunction has been reported in monogenic phenotypes, but also as part of common complex disorders. Explanations for the underlying mechanism of both disease types mostly focused on mutations in the open reading frames of proteins encoded by either the mitochondrial or nuclear genomes, as well as in tRNA or ribosomal RNA genes in the...

RNA-DNA differences (RDD) have previously been identified in the human mitochondrial RNA (mt-RNA) transcripts, yet their functional impact is poorly understood. By analyzing 4928 RNA-seq samples from 23 body sites, we found that mtDNA gene expression negatively correlated with the levels of both m1A 947 16 S rRNA modification (mtDNA position 2617)...

Background: Mitochondrial DNA (mtDNA) is present at high copy numbers in animal cells, and though characterized by a single haplotype in each individual due to maternal germline inheritance, deleterious mutations and intact mtDNA molecules frequently co-exist (heteroplasmy). A number of factors, such as replicative segregation, mitochondrial bottl...

Mitochondria are pivotal for bioenergetics, as well as in cellular response to viral infections. Nevertheless, their role in COVID-19 was largely overlooked. Here, we analyzed available bulk RNA-seq datasets from COVID-19 patients and corresponding healthy controls (three blood datasets, N=48 healthy, 119 patients; two respiratory tract datasets, N...

Recent advances in AI-based 3D protein structure prediction could help address health-related questions, but may also have far-reaching implications for evolution. Here we discuss the advantages and limitations of high-quality 3D structural predictions by AlphaFold2 in unravelling the relationship between protein properties and their impact on fitn...

Mitochondrial gene expression is pivotal to cell metabolism. Nevertheless, it is unknown whether it diverges within a given cell type. Here, we analysed single-cell RNA-seq experiments from human pancreatic alpha (N = 3471) and beta cells (N = 1989), as well as mouse beta cells (N = 1094). Cluster analysis revealed two distinct human beta cells pop...

Out of many intracellular bacteria, only the mitochondria and chloroplasts abandoned their independence billions of years ago and became endosymbionts within the host eukaryotic cell. Consequently, one cannot grow eukaryotic cells without their mitochondria, and the mitochondria cannot divide outside of the cell, thus reflecting interdependence. He...

In the Australian redclaw crayfish, Cherax quadricarinatus (WZ/ZZ system), intersexuals, although exhibiting both male and female gonopores, are functional males bearing a female genotype (WZ males). Therefore, the occurrence of the unusual homogametic WW females in nature is plausible. We developed W/Z genomic sex markers and used them to investig...

Mitochondrial gene expression is pivotal to cell metabolism. Nevertheless, it is unknown whether it diverges within a given cell type. Here, we analyzed single-cell RNA-seq experiments from ~4600 human pancreatic alpha and beta cells, as well as ~900 mouse beta cells. Cluster analysis revealed two distinct human beta cells populations, which diverg...

Dan Mishmar recounts the first studies that used mitochondrial DNA (mtDNA) to trace the origin of humanity to Africa and that connected mtDNA mutations with a human disease.

The higher order organization of eukaryotic and prokaryotic genomes is pivotal in the regulation of gene expression. Specifically, chromatin accessibility in eukaryotes and nucleoid accessibility in bacteria are regulated by a cohort of proteins to alter gene expression in response to diverse physiological conditions. By contrast, prior studies hav...

Natural selection acts on the phenotype. Therefore, many mistakenly expect to observe its signatures only in the organism, while overlooking its impact on tissues, cells and subcellular compartments. This is particularly crucial in the case of the mitochondrial genome (mtDNA), which, unlike the nucleus, resides in multiple cellular copies that may...

Mitochondrial complex I (CI) is the largest multi-subunit oxidative phosphorylation (OXPHOS) protein complex. Recent availability of a high-resolution human CI structure, and from two non-human mammals, enabled predicting the impact of mutations on interactions involving each of the 44 CI subunits. However, experimentally assessing the impact of th...

Deleterious and intact mitochondrial DNA (mtDNA) mutations frequently co-exist in cells (heteroplasmy). Such mutations likely survive and are inherited due to complementation via the intra-cellular mitochondrial network. Hence, we hypothesized that compromised mitochondrial fusion would hamper such complementation, thereby affecting heteroplasmy in...

Unlike the nuclear genome, the mammalian mitochondrial genome (mtDNA) is thought to be coated solely by mitochondrial transcription factor A (TFAM), whose binding sequence preferences are debated. Therefore, higher-order mtDNA organization is considered much less regulated than both the bacterial nucleoid and the nuclear chromatin. However, our rec...

Mitochondrial complex I (C1) is the largest multi-subunit oxidative phosphorylation (OXPHOS) protein complex. Recent availability of a high-resolution human C1 structure, and from two non-human mammals, enabled predicting the impact of mutations on interactions involving each of the 44 C1 subunits. However, experimentally assessing the impact of th...

Table S2. Calculated F-Scores for Mouse mt-ASFP Sites Per Mouse Embryonic Stage, Related to Figure 2 Last column represents mt-DGFs that co-localized with mt-ASFP sites.

Table S3. Calculated F-Scores for Mouse mt-DGF Sites Per Embryonic Stage, Related to Figure 2

mt-DGF sites that were present in more than 10% of the analyzed cell lines (N = 43) (according to Blumberg et al., 2018; Genome Research).

Expression quantitative trait loci (eQTLs) are instrumental in genome-wide identification of regulatory elements, yet were overlooked in the mitochondrial DNA (mtDNA). By analyzing 5079 RNA-seq samples from 23 tissues we identified association of ancient mtDNA SNPs (haplogroups T2, L2, J2 and V) and recurrent SNPs (mtDNA positions 263, 750, 1438 an...

Human mitochondrial DNA (mtDNA) is believed to lack chromatin and histones. Instead, it is coated solely by the transcription factor TFAM. We asked whether mtDNA packaging is more regulated than once thought. To address this, we analyzed DNase-seq experiments in 324 human cell types and found, for the first time, a pattern of 29 mtDNA Genomic footp...

Mitochondrial dysfunction has repeatedly been reported associated with type 2 diabetes mellitus (T2DM) and metabolic syndrome (MS), as have mitochondrial DNA (mtDNA) tRNA and duplication mutations and mtDNA haplogroup lineages. We identified 19 Taiwanese T2DM and MS pedigrees from Taiwan, with putative matrilineal transmission, one of which harbore...

Oxidative phosphorylation (OXPHOS), a fundamental energy source in all human tissues, requires interactions between mitochondrial (mtDNA) and nuclear (nDNA)-encoded protein subunits. Although such interactions are fundamental to OXPHOS, bi-genomic co-regulation is poorly understood. To address this question, we analyzed ~8,500 RNA-seq experiments f...

The bacterial heritage of mitochondria, as well as its independent genome [mitochondrial DNA (mtDNA)] and polycistronic transcripts, led to the view that mitochondrial transcriptional regulation relies on an evolutionarily conserved, prokaryotic-like system that is separated from the rest of the cell. Indeed, mtDNA transcription was previously thou...

The central role of the mitochondrion for cellular and organismal metabolism is well known, yet its functional role in evolution has rarely been featured in leading international conferences. Moreover, the contribution of mitochondrial genetics to complex disease phenotypes is particularly important, and although major advances have been made in th...

Human mitochondrial DNA (mtDNA) is believed to lack chromatin and histones. Instead, it is coated solely by the transcription factor TFAM, which binds the mtDNA without sequence specificity and packs it into a bacterial-like nucleoid in a dose-dependent fashion. We asked whether mtDNA packaging is more regulated than once thought. As a first step t...

In humans, oxidative phosphorylation (OXPHOS), the cellular energy producer, harbors ∼90 nuclear DNA (nDNA)- and mitochondrial DNA (mtDNA)-encoded subunits. Although nDNA- and mtDNA-encoded OXPHOS proteins physically interact, their transcriptional regulation profoundly diverges, thus questioning their co-regulation. To address mtDNA-nDNA gene co-e...

Human mtDNA genetic variants have traditionally been considered markers for ancient population migrations. However, during the past three decades, these variants have been associated with altered susceptibility to various phenotypes, thus supporting their importance for human health. Nevertheless, mtDNA disease association has frequently been suppo...

Many lineage-defining (nodal) mutations possess high functionality. However, differentiating adaptive nodal mutations from those that are functionally compensated remains challenging. To address this challenge, we identified functional nodal mutations (fNMs) in ~3,400 nuclear DNA (nDNA) and 4 mitochondrial DNA (mtDNA) protein structures from 91 and...

[This corrects the article DOI: 10.1371/journal.pbio.1002557.].

Originally published, uncorrected article. (PDF)

Republished, corrected article. (PDF)

Mitochondrial DNA (mtDNA) genes are long known to be co-transcribed in polycistrones, yet it remains impossible to study nascent mtDNA transcripts quantitatively in vivo using existing tools. To this end we used deep sequencing (GRO-seq and PRO-seq) and analyzed nascent mtDNA-encoded RNA transcripts in diverse human cell lines and metazoan organism...

The mitochondrion is the only organelle in animal cells with its own genome (mtDNA). Nevertheless, most mitochondrial proteins are encoded by the nuclear genome and are then imported into the mitochondria. Because animal mtDNA has a higher order of mutation rate compared to the nuclear genome, tight mitochondrial–nuclear coevolution is required to...

Mitochondrial DNA (mtDNA) variants have been traditionally used as markers to trace ancient population migrations. Although experiments relying on model organisms and cytoplasmic hybrids, as well as disease association studies, have served to underline the functionality of certain mtDNA SNPs, only little is known of the regulatory impact of ancient...

Phylogenetic analysis of the extracted mtDNA sequences from RNA-seq and corresponding DNA sequences. A comparison between phylogenetic trees (NJ), based on 454 reconstructed mtDNA sequence of the long RNA dataset (A), and 402 mtDNA sequences extracted from the same individuals, which were part of the 1000 Genomes Project (B). Branch colors indicate...

Comparison between expression analyses of mapping to chromosome M (rCRS) versus the mapping using the personalized mtDNA genomes. (A) Mapping of reads to rCRS (Chromosome M). (B) Mapping of reads against the personalized mtDNA genome of each sample. X axis–mtDNA genes, Y axis—normalized read count. Statistical significance: (*) p<3.7e-5; (**) p< 1e...

mtDNA eQTL test of the Africans long RNA dataset. Number of individuals per SNP is listed. Information indicated in columns E-H is available only for SNPs that passed the p-value cutoff after Bonferroni correction (5.84e-5) in the two tested groups. (XLSX)

nDNA eQTL test of the long RNA dataset. Information indicated in columns B-C is available only for SNPs that passed the p-value cutoff after Bonferroni correction (6.52e-6) in the two tested groups. (XLSX)

mtDNA eQTL test of the Caucasians tRNA dataset. Number of individuals per SNP is listed. Information indicated in columns E-H is available only for SNPs that passed the p-value cutoff after Bonferroni correction (3.95e-5) in the two tested groups. (XLSX)

Differentially expressed nDNA-encoded genes in L-haplogroup versus non-L haplogroup samples. Expression ratio of 2,380 differentially expressed nuclear genes in L versus non-L haplogroup samples. X axis represents the different genes, Y axis is the L/non-L ratio of the normalized read counts. (TIF)

List of nuclear genes that co-express with the mtDNA-encoded genes. (XLSX)

mtDNA eQTL test of the Africans tRNA dataset. Number of individuals per SNP is listed. Information indicated in columns E-H is available only for SNPs that passed the p-value cutoff after Bonferroni correction (5.48e-5) in the two tested groups. (XLSX)

Differential expression pattern between studies. Normalized read count of RNA-seq samples from different published studies for L haplogroups (A-C) and non-L haplogroups (D-F). The Lappalainen dataset [26] shares most of the samples from the Pickrell [28] and Montgomery [29] datasets. (A) and (D) display the expression pattern of all mtDNA genes. ND...

RNA read coverage of the mtDNA. Coverage of the mtDNA by the RNA reads for the long RNA dataset (A) and the tRNA dataset (B). X axis annotates the mtDNA positions, Y axis represents the different samples, and log10-transformed read count per position is represented by color (side bar). (TIF)

mtDNA eQTL test of the long RNA dataset. Number of individuals per SNP are listed. Information indicated in columns E-H is available only for SNPs that passed the p-value cutoff after Bonferroni correction (3.7e-5) in the two tested groups. (XLSX)

mtDNA eQTL test of the tRNA dataset. Number of individuals per SNP are listed. Information indicated in columns E-H is available only for SNPs that passed the p-value cutoff after Bonferroni correction (3.47e-5) in the two tested groups. (XLSX)

mtDNA eQTL test of the Caucasians long RNA dataset. Number of individuals per SNP is listed. Information indicated in columns E-H is available only for SNPs that passed the p-value cutoff after Bonferroni correction (4.22e-5) in the two tested groups. (XLSX)

Molecular function gene ontology (GO) annotation. (XLSX)

nDNA eQTL test of the tRNA dataset. Information indicated in columns B-C is available only for SNPs that passed the p-value cutoff after Bonferroni correction (6.11e-6) in the two tested groups. (XLSX)

Author RNA modifications constitute an important layer of information, with functional implications that are not written in the underlying DNA sequence. Recently, we observed an apparent RNA-DNA difference (RDD) at position 947 of the human mitochondrial 16S ribosomal RNA (rRNA), but its nature and mechanism were unclear. Here we show that this di...

Mitochondrial DNA (mtDNA) genes are long known to be co-transcribed in polycistrones, yet it remains impossible to study nascent mtDNA transcripts quantitatively in vivo using existing tools. To this end we used deep sequencing (GRO-seq and PRO-seq) and analyzed nascent mtDNA-encoded RNA transcripts in diverse human cell lines and metazoan organism...

RNA-seq is becoming a preferred tool for genomics studies of model and non-model organisms. However, DNA-based analysis of organisms lacking sequenced genomes cannot rely on RNA-seq data alone to isolate most genes of interest, as DNA codes both exons and introns. With this in mind, we designed a novel tool, LEMONS, that exploits the evolutionary c...

Compatibility between the nuclear (nDNA) and mitochondrial (mtDNA) genomes is important for organismal health. However, its significance for major evolutionary processes such as speciation is unclear, especially in vertebrates. We previously identified a sharp mtDNA-specific sequence divergence between morphologically indistinguishable chameleon po...

In contrast to the nuclear genome, the mitochondrial DNA (mtDNA) is maternally inherited and resides in multiple cellular copies that may vary in sequence (heteroplasmy). Although the interaction between mtDNA and nuclear DNA-encoded factors (mito-nuclear interaction) is vital, the mtDNA accumulates mutations an order of magnitude faster than the n...

Most cell functions are carried out by interacting factors, thus underlying the functional importance of genetic interactions between genes, termed epistasis. Epistasis could be under strong selective pressures especially in conditions where the mutation rate of one of the interacting partners notably differs from the other. Accordingly, the order...

Parkin, which is mutated in most recessive Parkinsonism, is a key player in the selective removal of damaged mitochondria via mitophagy. Damaged mitochondria may carry mitochondrial DNA (mtDNA) mutations, thus creating a mixed mtDNA population within cells (heteroplasmy). It was previously shown that Parkin over-expression reduced the level of hete...

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, w...

Transcription of mtDNA-encoded genes is thought to be regulated by a handful of dedicated transcription factors (TFs), suggesting that mtDNA genes are separately regulated from the nucleus. However, several TFs, with known nuclear activities, were found to bind mtDNA and regulate mitochondrial transcription. Additionally, mtDNA transcriptional regu...

Recently, we found dramatic mitochondrial DNA divergence of Israeli Chamaeleo chamaeleon populations into two geographically distinct groups. We aimed to examine whether the same pattern of divergence could be found in nuclear genes. However, no genomic resource is available for any chameleon species. Here we present the first chameleon transcripto...

RNA transcripts are generally identical to the underlying DNA sequences. Nevertheless, RNA-DNA differences (RDDs) were found in the nuclear human genome and in plants and animals but not in human mitochondria. Here by deep sequencing of human mitochondrial DNA (mtDNA) and RNA, we identified three RDD sites at mtDNA positions 295 (C-to-U), 13710 (A-...

Mutations frequently reoccur in the human mtDNA. However, it is unclear whether recurrent mtDNA nodal mutations (RNMs), i.e. recurrent mutations in stems of unrelated phylogenetic nodes, are functional and hence selectively constrained. To answer this question, we performed comprehensive parsimony and maximum likelihood analyses of 9,868 publicly a...

Heteroplasmy, the mixture of mitochondrial genomes (mtDNA), varies among individuals and