• Karczewski, K. J. et al. The mutational constraint spectrum quantified from variation in 141,456 humans. Nature 581, 434–443 (2020).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Havrilla, J. M., Pedersen, B. S., Layer, R. M. & Quinlan, A. R. A map of constrained coding regions in the human genome. Nat. Genet. 51, 88–95 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Samocha, K. E. et al. Regional missense constraint improves variant deleteriousness prediction. Preprint at BioRxiv https://doi.org/10.1101/148353 (2017).

  • Petrovski, S., Wang, Q., Heinzen, E. L., Allen, A. S. & Goldstein, D. B. Genic intolerance to functional variation and the interpretation of personal genomes. PLoS Genet. 9, e1003709 (2013).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Laricchia, K. M. et al. Mitochondrial DNA variation across 56,434 individuals in gnomAD. Genome Res. 32, 569–582 (2022).

    Article 
    PubMed 

    Google Scholar
     

  • McBride, H. M., Neuspiel, M. & Wasiak, S. Mitochondria: more than just a powerhouse. Curr. Biol. 16, R551–R560 (2006).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Stewart, J. B. & Chinnery, P. F. Extreme heterogeneity of human mitochondrial DNA from organelles to populations. Nat. Rev. Genet. 22, 106–118 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Chen, Y., Zhou, Z. & Min, W. Mitochondria, oxidative stress and innate immunity. Front. Physiol. 9, 1487 (2018).

    Article 
    PubMed 

    Google Scholar
     

  • Gray, M. W. Mitochondrial evolution. Cold Spring Harb. Perspect. Biol. 4, a011403 (2012).

    Article 
    PubMed 

    Google Scholar
     

  • Anderson, S. et al. Sequence and organization of the human mitochondrial genome. Nature 290, 457–465 (1981).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Gorman, G. S. et al. Mitochondrial diseases. Nat. Rev. Dis. Primers 2, 16080 (2016).

    Article 
    PubMed 

    Google Scholar
     

  • McCormick, E. M. et al. Specifications of the ACMG/AMP standards and guidelines for mitochondrial DNA variant interpretation. Hum. Mutat. 41, 2028–2057 (2020).

    Article 
    PubMed 

    Google Scholar
     

  • Wang, Y. et al. Association of mitochondrial DNA content, heteroplasmies and inter-generational transmission with autism. Nat. Commun. 13, 3790 (2022).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Gorelick, A. N. et al. Respiratory complex and tissue lineage drive recurrent mutations in tumour mtDNA. Nat. Metab. 3, 558–570 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Gopal, R. K. et al. Early loss of mitochondrial complex I and rewiring of glutathione metabolism in renal oncocytoma. Proc. Natl Acad. Sci. USA 115, E6283–E6290 (2018).

    Article 
    PubMed 

    Google Scholar
     

  • Kim, M., Mahmood, M., Reznik, E. & Gammage, P. A. Mitochondrial DNA is a major source of driver mutations in cancer. Trends Cancer 8, 1046–1059 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Keogh, M. J. & Chinnery, P. F. Mitochondrial DNA mutations in neurodegeneration. Biochim. Biophys. Acta 1847, 1401–1411 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Yonova-Doing, E. et al. An atlas of mitochondrial DNA genotype–phenotype associations in the UK Biobank. Nat. Genet. 53, 982–993 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kraja, A. T. et al. Associations of mitochondrial and nuclear mitochondrial variants and genes with seven metabolic traits. Am. J. Hum. Genet. 104, 112–138 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Yamamoto, K. et al. Genetic and phenotypic landscape of the mitochondrial genome in the Japanese population. Commun. Biol. 3, 104 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Stewart, J. B. et al. Strong purifying selection in transmission of mammalian mitochondrial DNA. PLoS Biol. 6, e10 (2008).

    Article 
    PubMed 

    Google Scholar
     

  • Voets, A. M. et al. Large scale mtDNA sequencing reveals sequence and functional conservation as major determinants of homoplasmic mtDNA variant distribution. Mitochondrion 11, 964–972 (2011).

    Article 
    MathSciNet 
    CAS 
    PubMed 

    Google Scholar
     

  • Elson, J. L., Turnbull, D. M. & Howell, N. Comparative genomics and the evolution of human mitochondrial DNA: assessing the effects of selection. Am. J. Hum. Genet. 74, 229–238 (2004).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kivisild, T. et al. The role of selection in the evolution of human mitochondrial genomes. Genetics 172, 373–387 (2006).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Wei, W. et al. Germline selection shapes human mitochondrial DNA diversity. Science 364, eaau6520 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ju, Y. S. et al. Origins and functional consequences of somatic mitochondrial DNA mutations in human cancer. eLife 3, e02935 (2014).

    Article 
    PubMed 

    Google Scholar
     

  • Dietlein, F. et al. Identification of cancer driver genes based on nucleotide context. Nat. Genet. 52, 208–218 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Bolze, A. et al. A catalog of homoplasmic and heteroplasmic mitochondrial DNA variants in humans. Preprint at BioRxiv https://doi.org/10.1101/798264 (2020).

  • Lott, M. T. et al. mtDNA variation and analysis using MITOMAP and MITOMASTER. Curr. Protoc. Bioinformatics 1, 1.23.21–21.23.26 (2013).


    Google Scholar
     

  • Lake, N. J., Compton, A. G., Rahman, S. & Thorburn, D. R. Leigh syndrome: one disorder, more than 75 monogenic causes. Ann. Neurol. 79, 190–203 (2016).

    Article 
    PubMed 

    Google Scholar
     

  • McFarland, R., Elson, J. L., Taylor, R. W., Howell, N. & Turnbull, D. M. Assigning pathogenicity to mitochondrial tRNA mutations: when “definitely maybe” is not good enough. Trends Genet. 20, 591–596 (2004).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Rebelo-Guiomar, P., Powell, C. A., Van Haute, L. & Minczuk, M. The mammalian mitochondrial epitranscriptome. Biochim. Biophys. Acta Gene Regul. Mech. 1862, 429–446 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Helm, M. et al. Search for characteristic structural features of mammalian mitochondrial tRNAs. RNA 6, 1356–1379 (2000).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Wong, L.-J. C. et al. Interpretation of mitochondrial tRNA variants. Genet. Med. 22, 917–926 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Amunts, A., Brown, A., Toots, J., Scheres, S. H. & Ramakrishnan, V. Ribosome. The structure of the human mitochondrial ribosome. Science 348, 95–98 (2015).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Zhao, H. et al. Maternally inherited aminoglycoside-induced and nonsyndromic deafness is associated with the novel C1494T mutation in the mitochondrial 12S rRNA gene in a large Chinese family. Am. J. Hum. Genet. 74, 139–152 (2004).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Nicholls, T. J. & Minczuk, M. In D-loop: 40 years of mitochondrial 7S DNA. Exp. Gerontol. 56, 175–181 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Horn, D. & Barrientos, A. Mitochondrial copper metabolism and delivery to cytochrome c oxidase. IUBMB Life 60, 421–429 (2008).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kampjut, D. & Sazanov, L. A. The coupling mechanism of mammalian respiratory complex I. Science 370, abc4209 (2020).

    Article 

    Google Scholar
     

  • Koripella, R. K., Sharma, M. R., Risteff, P., Keshavan, P. & Agrawal, R. K. Structural insights into unique features of the human mitochondrial ribosome recycling. Proc. Natl Acad. Sci. USA 116, 8283–8288 (2019).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Hong, Y. S. et al. Deleterious heteroplasmic mitochondrial mutations are associated with an increased risk of overall and cancer-specific mortality. Nat. Commun. 14, 6113 (2023).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Mok, B. Y. et al. CRISPR-free base editors with enhanced activity and expanded targeting scope in mitochondrial and nuclear DNA. Nat. Biotechnol. 40, 1378–1387 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Rajasimha, H. K., Chinnery, P. F. & Samuels, D. C. Selection against pathogenic mtDNA mutations in a stem cell population leads to the loss of the 3243A→G mutation in blood. Am. J. Hum. Genet. 82, 333–343 (2008).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Floros, V. I. et al. Segregation of mitochondrial DNA heteroplasmy through a developmental genetic bottleneck in human embryos. Nat. Cell Biol. 20, 144–151 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Zaidi, A. A. et al. Bottleneck and selection in the germline and maternal age influence transmission of mitochondrial DNA in human pedigrees. Proc. Natl Acad. Sci. USA 116, 25172–25178 (2019).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Schaefer, P. M. et al. Combination of common mtDNA variants results in mitochondrial dysfunction and a connective tissue dysregulation. Proc. Natl Acad. Sci. USA 119, e2212417119 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kennedy, S. R., Salk, J. J., Schmitt, M. W. & Loeb, L. A. Ultra-sensitive sequencing reveals an age-related increase in somatic mitochondrial mutations that are inconsistent with oxidative damage. PLoS Genet. 9, e1003794 (2013).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ludwig, L. S. et al. Lineage tracing in humans enabled by mitochondrial mutations and single-cell genomics. Cell 176, 1325–1339.e22 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Rebolledo-Jaramillo, B. et al. Maternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA. Proc. Natl Acad. Sci. USA 111, 15474–15479 (2014).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Li, M. et al. Transmission of human mtDNA heteroplasmy in the Genome of the Netherlands families: support for a variable-size bottleneck. Genome Res. 26, 417–426 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Yuan, Y. et al. Comprehensive molecular characterization of mitochondrial genomes in human cancers. Nat. Genet. 52, 342–352 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • SPARK Consortium. SPARK: A US cohort of 50,000 families to accelerate autism research. Neuron 97, 488–493 (2018).

    Article 

    Google Scholar
     

  • Colnaghi, M., Pomiankowski, A. & Lane, N. The need for high-quality oocyte mitochondria at extreme ploidy dictates mammalian germline development. eLife 10, e69344 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Van Oven, M. PhyloTree Build 17: Growing the human mitochondrial DNA tree. Forensic Sci. Int. Genet. Suppl. Ser. 5, e392–e394 (2015).

    Article 

    Google Scholar
     

  • Lake, N. J., Zhou, L., Xu, J. & Lek, M. MitoVisualize: a resource for analysis of variants in human mitochondrial RNAs and DNA. Bioinformatics 38, 2967–2969 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Bodenhofer, U., Bonatesta, E., Horejs-Kainrath, C. & Hochreiter, S. msa: an R package for multiple sequence alignment. Bioinformatics 31, 3997–3999 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • UniProt, C. UniProt: a worldwide hub of protein knowledge. Nucleic Acids Res. 47, D506–D515 (2019).

    Article 

    Google Scholar
     

  • Sonney, S. et al. Predicting the pathogenicity of novel variants in mitochondrial tRNA with MitoTIP. PLoS Comput. Biol. 13, e1005867 (2017).

    Article 
    PubMed 

    Google Scholar
     

  • Landrum, M. J. et al. ClinVar: improving access to variant interpretations and supporting evidence. Nucleic Acids Res. 46, D1062–D1067 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Akesson, L. S. et al. Early diagnosis of Pearson syndrome in neonatal intensive care following rapid mitochondrial genome sequencing in tandem with exome sequencing. Eur. J. Hum. Genet. 27, 1821–1826 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Davydov, E. V. et al. Identifying a high fraction of the human genome to be under selective constraint using GERP++. PLoS Comput. Biol. 6, e1001025 (2010).

    Article 
    PubMed 

    Google Scholar
     

  • Hamelryck, T. & Manderick, B. PDB file parser and structure class implemented in Python. Bioinformatics 19, 2308–2310 (2003).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Guo, R., Zong, S., Wu, M., Gu, J. & Yang, M. Architecture of human mitochondrial respiratory megacomplex I2III2IV2. Cell 170, 1247–1257.e12 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Zong, S. et al. Structure of the intact 14-subunit human cytochrome c oxidase. Cell Res. 28, 1026–1034 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Aibara, S., Singh, V., Modelska, A. & Amunts, A. Structural basis of mitochondrial translation. eLife 9, e58362 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Soltanikazemi, E., Quadir, F., Roy, R. S., Guo, Z. & Cheng, J. Distance-based reconstruction of protein quaternary structures from inter-chain contacts. Proteins 90, 720–731 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Pettersen, E. F. et al. UCSF ChimeraX: structure visualization for researchers, educators, and developers. Protein Sci. 30, 70–82 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Sudlow, C. et al. UK Biobank: an open access resource for identifying the causes of a wide range of complex diseases of middle and old age. PLoS Med. 12, e1001779 (2015).

    Article 
    PubMed 

    Google Scholar
     

  • Battle, S. L. et al. A bioinformatics pipeline for estimating mitochondrial DNA copy number and heteroplasmy levels from whole genome sequencing data. NAR Genom. Bioinform. 4, lqac034 (2022).

    Article 
    PubMed 

    Google Scholar
     

  • Cacheiro, P. et al. Human and mouse essentiality screens as a resource for disease gene discovery. Nat. Commun. 11, 655 (2020).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Firth, H. V. et al. DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources. Am. J. Hum. Genet. 84, 524–533 (2009).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Lake, N., Ma, K. Cohen, J., Lek, M. Mitochondrial DNA base editing in HEK293T cells. protocols.io https://doi.org/10.17504/protocols.io.yxmvm3rnol3p/v1 (2024).

  • Kluesner, M. G. et al. EditR: a method to quantify base editing from Sanger sequencing. CRISPR J. 1, 239–250 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Mok, B. Y. et al. A bacterial cytidine deaminase toxin enables CRISPR-free mitochondrial base editing. Nature 583, 631–637 (2020).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     



  • Source link

    Leave a Reply

    Your email address will not be published. Required fields are marked *