Nass, S. & Nass, M. M. K. Intramitochondrial fibers with DNA characteristics: II. Enzymatic and other hydrolytic treatments. J. Cell Biol. 19, 613 (1963).
Wallace, D. C. Why do we still have a maternally inherited mitochondrial DNA? Insights from evolutionary medicine. Annu. Rev. Biochem. 76, 781–821 (2007).
Stewart, J. B. & Chinnery, P. F. The dynamics of mitochondrial DNA heteroplasmy: implications for human health and disease. Nat. Rev. Genet. 16, 530–542 (2015).
Wai, T. et al. The role of mitochondrial DNA copy number in mammalian fertility. Biol. Reprod. 83, 52–62 (2010).
Palis, J. Primitive and definitive erythropoiesis in mammals. Front. Physiol. 5, 3 (2014).
Gupta, R. et al. Nuclear genetic control of mtDNA copy number and heteroplasmy in humans. Nature 620, 839–848 (2023).
Stewart, J. B. & Chinnery, P. F. Extreme heterogeneity of human mitochondrial DNA from organelles to populations. Nat. Rev. Genet. 22, 106–118 (2021).
Emery, L. S., Magnaye, K. M., Bigham, A. W., Akey, J. M. & Bamshad, M. J. Estimates of continental ancestry vary widely among individuals with the same mtDNA haplogroup. Am. J. Hum. Genet. 96, 183–193 (2015).
Kandasamy, J., Rezonzew, G., Jilling, T., Ballinger, S. & Ambalavanan, N. Mitochondrial DNA variation modulates alveolar development in newborn mice exposed to hyperoxia. Am. J. Physiol. Lung Cell. Mol. Physiol. 317, L740–L747 (2019).
Farha, S. et al. Mitochondrial haplogroups and risk of pulmonary arterial hypertension. PLoS ONE 11, e0156042 (2016).
Kenney, M. C. et al. Molecular and bioenergetic differences between cells with African versus European inherited mitochondrial DNA haplogroups: implications for population susceptibility to diseases. Biochim. Biophys. Acta 1842, 208–219 (2014).
Campbell, P. et al. Mitochondrial mutation, drift and selection during human development and ageing. Preprint at Research Square https://doi.org/10.21203/rs.3.rs-3083262/v1 (2023).
Pesole, G., Gissi, C., De Chirico, A. & Saccone, C. Nucleotide substitution rate of mammalian mitochondrial genomes. J. Mol. Evol. 48, 427–434 (1999).
Haag-Liautard, C. et al. Direct estimation of the mitochondrial DNA mutation rate in Drosophila melanogaster. PLoS Biol. 6, e204 (2008).
Wallace, D. C. Mitochondrial genetic medicine. Nat. Genet. 50, 1642–1649 (2018).
Yonova-Doing, E. et al. An atlas of mitochondrial DNA genotype–phenotype associations in the UK Biobank. Nat. Genet. 53, 982–993 (2021).
Cai, N. et al. Mitochondrial DNA variants modulate N-formylmethionine, proteostasis and risk of late-onset human diseases. Nat. Med. 27, 1564–1575 (2021).
Gorelick, A. N. et al. Respiratory complex and tissue lineage drive recurrent mutations in tumour mtDNA. Nat. Metab. 3, 558–570 (2021).
Triska, P. et al. Landscape of germline and somatic mitochondrial DNA mutations in pediatric malignancies. Cancer Res. 79, 1318–1330 (2019).
Kopinski, P. K., Singh, L. N., Zhang, S., Lott, M. T. & Wallace, D. C. Mitochondrial DNA variation and cancer. Nat. Rev. Cancer 21, 431–445 (2021).
Yuan, Y. et al. Comprehensive molecular characterization of mitochondrial genomes in human cancers. Nat. Genet. 52, 342–352 (2020).
Mahmood, M. et al. Mitochondrial DNA mutations drive aerobic glycolysis to enhance checkpoint blockade response in melanoma. Nat. Cancer https://doi.org/10.1038/s43018-023-00721-w (2024)
Suomalainen, A. & Battersby, B. J. Mitochondrial diseases: the contribution of organelle stress responses to pathology. Nat. Rev. Mol. Cell Biol. 19, 77–92 (2017).
Rood, J. E., Maartens, A., Hupalowska, A., Teichmann, S. A. & Regev, A. Impact of the human cell atlas on medicine. Nat. Med. 28, 2486–2496 (2022).
Rajewsky, N. et al. LifeTime and improving European healthcare through cell-based interceptive medicine. Nature 587, 377–386 (2020).
Lodato, M. A. et al. Somatic mutation in single human neurons tracks developmental and transcriptional history. Science 350, 94–98 (2015).
Luquette, L. J. et al. Single-cell genome sequencing of human neurons identifies somatic point mutation and indel enrichment in regulatory elements. Nat. Genet. 54, 1564–1571 (2022).
Ludwig, L. S. et al. Lineage tracing in humans enabled by mitochondrial mutations and single-cell genomics. Cell 176, 1325–1339.e22 (2019).
Xu, J. et al. Single-cell lineage tracing by endogenous mutations enriched in transposase accessible mitochondrial DNA. eLife 8, e45105 (2019).
Picelli, S. et al. Full-length RNA-seq from single cells using Smart-seq2. Nat. Protoc. 9, 171–181 (2014).
Hagemann-Jensen, M. et al. Single-cell RNA counting at allele and isoform resolution using Smart-seq3. Nat. Biotechnol. 38, 708–714 (2020).
Hagemann-Jensen, M., Ziegenhain, C. & Sandberg, R. Scalable single-cell RNA sequencing from full transcripts with Smart-seq3xpress. Nat. Biotechnol. 40, 1452–1457 (2022).
Hahaut, V. et al. Fast and highly sensitive full-length single-cell RNA sequencing using FLASH-seq. Nat. Biotechnol. 40, 1447–1451 (2022).
Zheng, G. X. Y. et al. Massively parallel digital transcriptional profiling of single cells. Nat. Commun. 8, 1–12 (2017).
Miller, T. E. et al. Mitochondrial variant enrichment from high-throughput single-cell RNA sequencing resolves clonal populations. Nat. Biotechnol. 40, 1030–1034 (2022).
Gier, R. A. et al. Clonal cell states link Barrett’s esophagus and esophageal adenocarcinoma. Preprint at bioRxiv https://doi.org/10.1101/2023.01.26.525564 (2023).
Salmen, F. et al. High-throughput total RNA sequencing in single cells using VASA-seq. Nat. Biotechnol. 40, 1780–1793 (2022).
Lareau, C. A. et al. Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling. Nat. Biotechnol. 39, 451–461 (2021).
Stefan Isaac, R. et al. Single-nucleoid architecture reveals heterogeneous packaging of mitochondrial DNA. Nat. Struct. Mol. Biol. 31, 568–577 (2024).
Mimitou, E. P. et al. Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells. Nat. Biotechnol. 39, 1246–1258 (2021).
Fiskin, E. et al. Single-cell profiling of proteins and chromatin accessibility using PHAGE-ATAC. Nat. Biotechnol. 40, 374–381 (2021).
Izzo, F. et al. Mapping genotypes to chromatin accessibility profiles in single cells. Nature 629, 1149–1157 (2024).
Weng, C. et al. Deciphering cell states and genealogies of human hematopoiesis. Nature https://doi.org/10.1038/s41586-024-07066-z (2024).
Gerstung, M. et al. The evolutionary history of 2,658 cancers. Nature 578, 122–128 (2020).
Sankaran, V. G., Weissman, J. S. & Zon, L. I. Cellular barcoding to decipher clonal dynamics in disease. Science 378, eabm5874 (2022).
Spencer Chapman, M. et al. Lineage tracing of human development through somatic mutations. Nature 595, 85–90 (2021).
Mitchell, E. et al. Clonal dynamics of haematopoiesis across the human lifespan. Nature 606, 343–350 (2022).
Picca, A., Faitg, J., Auwerx, J., Ferrucci, L. & D’Amico, D. Mitophagy in human health, ageing and disease. Nat. Metab. 5, 2047–2061 (2023).
Fellous, T. G. et al. Locating the stem cell niche and tracing hepatocyte lineages in human liver. Hepatology 49, 1655–1663 (2009).
Taylor, R. W. et al. Mitochondrial DNA mutations in human colonic crypt stem cells. J. Clin. Invest. 112, 1351–1360 (2003).
Teixeira, V. H. et al. Stochastic homeostasis in human airway epithelium is achieved by neutral competition of basal cell progenitors. eLife 2, e00966 (2013).
Blackwood, J. K. et al. In situ lineage tracking of human prostatic epithelial stem cell fate reveals a common clonal origin for basal and luminal cells. J. Pathol. 225, 181–188 (2011).
Cereser, B. et al. Analysis of clonal expansions through the normal and premalignant human breast epithelium reveals the presence of luminal stem cells. J. Pathol. 244, 61–70 (2018).
Tempest, N. et al. Histological 3D reconstruction and in vivo lineage tracing of the human endometrium. J. Pathol. 251, 440–451 (2020).
Rodriguez-Fraticelli, A. E. et al. Clonal analysis of lineage fate in native haematopoiesis. Nature 553, 212–216 (2018).
Li, L. et al. A mouse model with high clonal barcode diversity for joint lineage, transcriptomic, and epigenomic profiling in single cells. Cell 186, 5183–5199.e22 (2023).
Ferrari, S. et al. Efficient gene editing of human long-term hematopoietic stem cells validated by clonal tracking. Nat. Biotechnol. 38, 1298–1308 (2020).
Lareau, C. A., Ludwig, L. S. & Sankaran, V. G. Longitudinal assessment of clonal mosaicism in human hematopoiesis via mitochondrial mutation tracking. Blood Adv. 3, 4161–4165 (2019).
Liu, D. et al. Intercellular mitochondrial transfer as a means of tissue revitalization. Signal Transduct. Target Ther. 6, 65 (2021).
Zhang, H. et al. Systematic investigation of mitochondrial transfer between cancer cells and T cells at single-cell resolution. Cancer Cell 41, 1788–1802.e10 (2023).
Beneyto-Calabuig, S. et al. Clonally resolved single-cell multi-omics identifies routes of cellular differentiation in acute myeloid leukemia. Cell Stem Cell 30, 706–721.e8 (2023).
Lee-Six, H. et al. Population dynamics of normal human blood inferred from somatic mutations. Nature 561, 473–478 (2018).
Haghverdi, L. & Ludwig, L. S. Single-cell multi-omics and lineage tracing to dissect cell fate decision-making. Stem Cell Rep. 18, 13–25 (2023).
Weinreb, C., Rodriguez-Fraticelli, A., Camargo, F. D. & Klein, A. M. Lineage tracing on transcriptional landscapes links state to fate during differentiation. Science 367, eaaw3381 (2020).
Fearon, E. R. & Vogelstein, B. A genetic model for colorectal tumorigenesis. Cell 61, 759–767 (1990).
Penter, L. et al. Longitudinal single-cell dynamics of chromatin accessibility and mitochondrial mutations in chronic lymphocytic leukemia mirror disease history. Cancer Discov. 11, 3048–3063 (2021).
Poos, A. M. et al. Resolving therapy resistance mechanisms in multiple myeloma by multi-omics subclone analysis. Blood https://doi.org/10.1182/blood.2023019758 (2023)
Nam, A. S. et al. Single-cell multi-omics of human clonal hematopoiesis reveals that DNMT3A R882 mutations perturb early progenitor states through selective hypomethylation. Nat. Genet. 54, 1514–1526 (2022).
Adams, N. M., Grassmann, S. & Sun, J. C. Clonal expansion of innate and adaptive lymphocytes. Nat. Rev. Immunol. 20, 694–707 (2020).
Jenkins, M. K., Chu, H. H., McLachlan, J. B. & Moon, J. J. On the composition of the preimmune repertoire of T cells specific for peptide-major histocompatibility complex ligands. Annu. Rev. Immunol. 28, 275–294 (2010).
Schatz, D. G. & Ji, Y. Recombination centres and the orchestration of V(D)J recombination. Nat. Rev. Immunol. 11, 251–263 (2011).
Yost, K. E. et al. Clonal replacement of tumor-specific T cells following PD-1 blockade. Nat. Med. 25, 1251–1259 (2019).
Musvosvi, M. et al. T cell receptor repertoires associated with control and disease progression following Mycobacterium tuberculosis infection. Nat. Med. 29, 258–269 (2023).
Rückert, T., Lareau, C. A., Mashreghi, M.-F., Ludwig, L. S. & Romagnani, C. Clonal expansion and epigenetic inheritance of long-lasting NK cell memory. Nat. Immunol. 23, 1551–1563 (2022).
Walker, M. A. et al. Purifying selection against pathogenic mitochondrial DNA in human T cells. N. Engl. J. Med. 383, 1556–1563 (2020).
Glynos, A. et al. High-throughput single-cell analysis reveals progressive mitochondrial DNA mosaicism throughout life. Sci. Adv. 9, eadi4038 (2023).
Rossignol, R. et al. Mitochondrial threshold effects. Biochem. J. 370, 751–762 (2003).
Lareau, C. A. et al. Single-cell multi-omics of mitochondrial DNA disorders reveals dynamics of purifying selection across human immune cells. Nat. Genet. 55, 1198–1209 (2023).
Franklin, I. G. et al. T cell differentiation drives the negative selection of pathogenic mitochondrial DNA variants. Life Sci. Alliance 6, e202302271 (2023).
Zhang, J. et al. Antigen receptor stimulation induces purifying selection against pathogenic mitochondrial tRNA mutations. JCI Insight 8, e167656 (2023).
Cree, L. M. et al. A reduction of mitochondrial DNA molecules during embryogenesis explains the rapid segregation of genotypes. Nat. Genet. 40, 249–254 (2008).
Cao, L. et al. The mitochondrial bottleneck occurs without reduction of mtDNA content in female mouse germ cells. Nat. Genet. 39, 386–390 (2007).
Burr, S. P. et al. Cell lineage-specific mitochondrial resilience during mammalian organogenesis. Cell 186, 1212–1229.e21 (2023).
Trifunovic, A. et al. Premature ageing in mice expressing defective mitochondrial DNA polymerase. Nature 429, 417–423 (2004).
Kujoth, G. C. et al. Mitochondrial DNA mutations, oxidative stress, and apoptosis in mammalian aging. Science 309, 481–484 (2005).
Nissanka, N. & Moraes, C. T. Mitochondrial DNA damage and reactive oxygen species in neurodegenerative disease. FEBS Lett. 592, 728–742 (2018).
Latorre-Pellicer, A. et al. Mitochondrial and nuclear DNA matching shapes metabolism and healthy ageing. Nature 535, 561–565 (2016).
Scotece, M. et al. Mitochondrial DNA impact on joint damaged process in a conplastic mouse model after being surgically induced with osteoarthritis. Sci. Rep. 11, 1–12 (2021).
Jacoby, E. et al. Mitochondrial augmentation of hematopoietic stem cells in children with single large-scale mitochondrial DNA deletion syndromes. Sci. Transl. Med. https://doi.org/10.1126/scitranslmed.abo3724 (2022).
Mok, B. Y. et al. A bacterial cytidine deaminase toxin enables CRISPR-free mitochondrial base editing. Nature 583, 631–637 (2020).
Ludwig, L. S. & Lareau, C. A. In Chromatin Accessibility: Methods and Protocols (eds Marinov, G. K. & Greenleaf, W. J.) 269–282 (Humana, 2023).
Ulirsch, J. C. et al. Interrogation of human hematopoiesis at single-cell and single-variant resolution. Nat. Genet. 51, 683–693 (2019).
Baysoy, A., Bai, Z., Satija, R. & Fan, R. The technological landscape and applications of single-cell multi-omics. Nat. Rev. Mol. Cell Biol. 24, 695–713 (2023).
Pai, J. A. & Satpathy, A. T. High-throughput and single-cell T cell receptor sequencing technologies. Nat. Methods 18, 881–892 (2021).
Lareau, C. A. et al. Mitochondrial single-cell ATAC-seq for high-throughput multi-omic detection of mitochondrial genotypes and chromatin accessibility. Nat. Protoc. 18, 1416–1440 (2023).
Buenrostro, J. D. et al. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature 523, 486–490 (2015).
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