Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition

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Chromatin is reprogrammed after fertilization to produce a totipotent zygote with the potential to generate a new organism1. The maternal genome inherited from the oocyte and the paternal genome provided by sperm coexist as separate haploid nuclei in the zygote. How these two epigenetically distinct genomes are spatially organized is poorly understood. Existing chromosome conformation capture-based methods2,3,4,5 are not applicable to oocytes and zygotes owing to a paucity of material. To study three-dimensional chromatin organization in rare cell types, we developed a single-nucleus Hi-C (high-resolution chromosome conformation capture) protocol that provides greater than tenfold more contacts per cell than the previous method2. Here we show that chromatin architecture is uniquely reorganized during the oocyte-to-zygote transition in mice and is distinct in paternal and maternal nuclei within single-cell zygotes. Features of genomic organization including compartments, topologically associating domains (TADs) and loops are present in individual oocytes when averaged over the genome, but the presence of each feature at a locus varies between cells. At the sub-megabase level, we observed stochastic clusters of contacts that can occur across TAD boundaries but average into TADs. Notably, we found that TADs and loops, but not compartments, are present in zygotic maternal chromatin, suggesting that these are generated by different mechanisms. Our results demonstrate that the global chromatin organization of zygote nuclei is fundamentally different from that of other interphase cells. An understanding of this zygotic chromatin ‘ground state’ could potentially provide insights into reprogramming cells to a state of totipotency.

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We thank C. Theußl for help with pronuclear extraction procedure, S. Ladstätter for assistance in scoring oocyte stages and K. Klien for experimental support and mouse colony management. We are grateful to I. Adams, S. Boyle, I. Vassias-Jossic, G. Almouzni and W. Bickmore for advice and help with FISH experiments. Illumina sequencing was performed at the VBCF NGS Unit (http://www.vbcf.ac.at) except Hi-C libraries from MEL cells, which were sequenced in the Laboratory of Evolutionary Genomics of the Faculty of Bioengineering and Bioinformatics, Moscow State University, by M. Logacheva. K562 cells were a gift from Alexander Stark laboratory. We thank the staff of the Institute of Genetics and Molecular Medicine imaging facility and Vienna Biocenter BioOptics facility for assistance with imaging and analysis. We thank all members of the K.T.-K. laboratory for discussions, Life Science Editors for editorial assistance and R. Illingworth for critically reading the manuscript. J.G. is an associated student of the DK Chromosome Dynamics supported by the grant W1238-B20 from the Austrian Science Fund (FWF). H.B.B. was partly supported by the Natural Sciences and Engineering Research Council of Canada, PGS-D. This work was funded by the Austrian Academy of Sciences and by the European Research Council (ERC-StG-336460 ChromHeritance) to K.T.-K. as well as by a grant from the Russian Science Foundation (14-24-00022) to S.V.U. and S.V.R. The work in the Mirny laboratory is supported by R01 GM114190, U54 DK107980 from the National Institute of Health, and 1504942 from the National Science Foundation.

Author information

Author notes

    • Ilya M. Flyamer

    Present address: MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK.

    • Leonid A. Mirny
    •  & Kikuë Tachibana-Konwalski

    These authors jointly supervised this work.

    • Ilya M. Flyamer
    • , Johanna Gassler
    •  & Maxim Imakaev

    These authors contributed equally to this work.


  1. IMBA - Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr Bohr-Gasse 3, 1030 Vienna, Austria

    • Ilya M. Flyamer
    • , Johanna Gassler
    •  & Kikuë Tachibana-Konwalski
  2. Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia

    • Ilya M. Flyamer
    • , Sergey V. Ulianov
    •  & Sergey V. Razin
  3. Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia

    • Ilya M. Flyamer
    • , Sergey V. Ulianov
    •  & Sergey V. Razin
  4. Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA

    • Maxim Imakaev
    •  & Leonid A. Mirny
  5. Department of Physics, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA

    • Maxim Imakaev
    •  & Leonid A. Mirny
  6. Harvard Program in Biophysics, Harvard University, Cambridge, Massachusetts 02138, USA

    • Hugo B. Brandão
    •  & Leonid A. Mirny
  7. Computational and Systems Biology Program, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139 USA

    • Nezar Abdennur


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I.M.F., J.G. and M.I. contributed equally and are listed alphabetically. K.T.-K. conceived the project. I.M.F., M.I., S.V.U. and K.T.-K. conceived the method. I.M.F. developed the method. I.M.F. and J.G., supervised by K.T.-K., performed snHi-C on oocytes and zygotes. S.V.U. supervised by S.V.R. and K.T.-K. performed scHi-C on K562 cells. I.M.F. supervised by S.V.R. performed in situ Hi-C on MEL cells. I.M.F. supervised by K.T-K performed 3D FISH on ES cells. J.G. supervised by K.T-K performed 3D FISH on zygotes. N.A. developed and maintains the library ‘lavaburst’ for TAD calling. M.I. and H.B.B. supervised by L.A.M. developed and performed snHi-C data analysis. H.B.B. led FISH data analysis and performed contact cluster analysis. M.I. performed simulations, processed the data, and performed genome-wide averaging analyses. M.I., H.B.B., I.M.F. and J.G. prepared the figures. M.I., I.M.F., J.G., H.B.B., L.A.M. and K.T.-K. wrote the manuscript with input from all authors.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Leonid A. Mirny or Kikuë Tachibana-Konwalski.

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    Supplementary Information

    This file contains Supplementary Methods, Supplementary References and Supplementary Table 1.


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