Segregation of mitochondrial DNA heteroplasmy through a developmental genetic bottleneck in human embryos

  • Nature Cell Biologyvolume 20pages144151 (2018)
  • doi:10.1038/s41556-017-0017-8
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Mitochondrial DNA (mtDNA) mutations cause inherited diseases and are implicated in the pathogenesis of common late-onset disorders, but how they arise is not clear1,2. Here we show that mtDNA mutations are present in primordial germ cells (PGCs) within healthy female human embryos. Isolated PGCs have a profound reduction in mtDNA content, with discrete mitochondria containing ~5 mtDNA molecules. Single-cell deep mtDNA sequencing of in vivo human female PGCs showed rare variants reaching higher heteroplasmy levels in late PGCs, consistent with the observed genetic bottleneck. We also saw the signature of selection against non-synonymous protein-coding, tRNA gene and D-loop variants, concomitant with a progressive upregulation of genes involving mtDNA replication and transcription, and linked to a transition from glycolytic to oxidative metabolism. The associated metabolic shift would expose deleterious mutations to selection during early germ cell development, preventing the relentless accumulation of mtDNA mutations in the human population predicted by Muller’s ratchet. Mutations escaping this mechanism will show shifts in heteroplasmy levels within one human generation, explaining the extreme phenotypic variation seen in human pedigrees with inherited mtDNA disorders.

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P.F.C. is a Wellcome Trust Senior Fellow in Clinical Science (101876/Z/13/Z), and a UK NIHR Senior Investigator, who receives support from the Medical Research Council Mitochondrial Biology Unit (MC_UP_1501/2), the Medical Research Council (UK) Centre for Translational Muscle Disease research (G0601943) and the National Institute for Health Research (NIHR) Biomedical Research Centre based at Cambridge University Hospitals NHS Foundation Trust and the University of Cambridge. The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR or the Department of Health. W.W.C.T. is supported by a Croucher Foundation studentship, and M.A.S. by a Wellcome Investigator Award.

Author information

Author notes

  1. Vasileios I. Floros and Angela Pyle contributed equally to this work.


  1. MRC-Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK

    • Vasileios I. Floros
    • , Wei Wei
    •  & Patrick F. Chinnery
  2. Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK

    • Vasileios I. Floros
    • , Wei Wei
    •  & Patrick F. Chinnery
  3. Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK

    • Angela Pyle
  4. Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK

    • Sabine Dietmann
    • , Brendan Payne
    • , Jonathan Coxhead
    •  & Gavin Hudson
  5. Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK

    • Walfred W. C. Tang
    • , Naoko Irie
    •  & M. Azim Surani
  6. GENERA, Centre for Reproductive Medicine, Clinica Valle Giulia, Rome, Italy

    • Antonio Capalbo
  7. GENETYX, Reproductive Genetics Laboratory, Marostica, Italy

    • Antonio Capalbo
  8. Division of Women’s Health, Faculty of Life Sciences and Medicine, King’s College London, London, UK

    • Laila Noli
    • , Yacoub Khalaf
    •  & Dusko Ilic
  9. Assisted Conception Unit, Guy’s Hospital, London, UK

    • Laila Noli
    • , Yacoub Khalaf
    •  & Dusko Ilic
  10. Human Developmental Biology Resource, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK

    • Moira Crosier
  11. Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK

    • Henrik Strahl
  12. Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan

    • Mitinori Saitou
  13. JST, ERATO, Kyoto, Japan

    • Mitinori Saitou


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V.I.F. developed methods and isolated the in vivo human and mouse PGCs, and performed the microscopy; S.D. performed RNA-seq bioinformatic analysis; A.P. and W.W.C.T. carried out the real-time PCR assays; W.W.C.T. performed the RNA-seq experiments and N.I. derived and isolated the hESCs, hPGCLCs and in vitro somatic cells; W.W. performed additional informatic and statistical analysis; A.C. and L.N. isolated the human inner cell mass and trophectoderm cells, overseen by D.I. and Y.K. J.C. carried out the library preparation and deep sequencing; M.C. helped with the human tissue dissection; H.S. helped with the super-resolution microscopy; B.P. performed the technical validation of the deep sequencing protocol; M.S. provided the BVSC mouse; G.H. advised on the NGS data analysis; M.A.S. supervised the RNA-seq experiments and real-time PCR expression assays and advised on the project; P.F.C. supervised the project, designed experiments, analysed the data and wrote the paper. All authors contributed to the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Patrick F. Chinnery.

Supplementary information

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