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

Author

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  • Ilya M. Flyamer

    (IMBA - Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter (VBC)
    Institute of Gene Biology, Russian Academy of Sciences
    Faculty of Biology, Lomonosov Moscow State University
    †Present address: MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK.)

  • Johanna Gassler

    (IMBA - Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter (VBC))

  • Maxim Imakaev

    (Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT)
    Massachusetts Institute of Technology (MIT))

  • Hugo B. Brandão

    (Harvard Program in Biophysics, Harvard University)

  • Sergey V. Ulianov

    (Institute of Gene Biology, Russian Academy of Sciences
    Faculty of Biology, Lomonosov Moscow State University)

  • Nezar Abdennur

    (Computational and Systems Biology Program, Massachusetts Institute of Technology (MIT),)

  • Sergey V. Razin

    (Institute of Gene Biology, Russian Academy of Sciences
    Faculty of Biology, Lomonosov Moscow State University)

  • Leonid A. Mirny

    (Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT)
    Massachusetts Institute of Technology (MIT)
    Harvard Program in Biophysics, Harvard University)

  • Kikuë Tachibana-Konwalski

    (IMBA - Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter (VBC))

Abstract

Using a single-nucleus Hi-C protocol, the authors find that spatial organization of chromatin during oocyte-to-zygote transition differs between paternal and maternal nuclei within a single-cell zygote.

Suggested Citation

  • Ilya M. Flyamer & Johanna Gassler & Maxim Imakaev & Hugo B. Brandão & Sergey V. Ulianov & Nezar Abdennur & Sergey V. Razin & Leonid A. Mirny & Kikuë Tachibana-Konwalski, 2017. "Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition," Nature, Nature, vol. 544(7648), pages 110-114, April.
    • Handle: RePEc:nat:nature:v:544:y:2017:i:7648:d:10.1038_nature21711
    DOI: 10.1038/nature21711
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    Citations

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    Cited by:

    1. Surya K Ghosh & Daniel Jost, 2018. "How epigenome drives chromatin folding and dynamics, insights from efficient coarse-grained models of chromosomes," PLOS Computational Biology, Public Library of Science, vol. 14(5), pages 1-26, May.
    2. Markus Götz & Olivier Messina & Sergio Espinola & Jean-Bernard Fiche & Marcelo Nollmann, 2022. "Multiple parameters shape the 3D chromatin structure of single nuclei at the doc locus in Drosophila," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    3. Varvara Lukyanchikova & Miroslav Nuriddinov & Polina Belokopytova & Alena Taskina & Jiangtao Liang & Maarten J. M. F. Reijnders & Livio Ruzzante & Romain Feron & Robert M. Waterhouse & Yang Wu & Chunh, 2022. "Anopheles mosquitoes reveal new principles of 3D genome organization in insects," Nature Communications, Nature, vol. 13(1), pages 1-22, December.
    4. Jason Alexander Halliwell & Javier Martin-Gonzalez & Adnan Hashim & John Arne Dahl & Eva R. Hoffmann & Mads Lerdrup, 2024. "Sex-specific DNA-replication in the early mammalian embryo," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    5. Guang Shi & D. Thirumalai, 2023. "A maximum-entropy model to predict 3D structural ensembles of chromatin from pairwise distances with applications to interphase chromosomes and structural variants," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    6. Shuangyi Xu & Ning Wang & Michael V. Zuccaro & Jeannine Gerhardt & Rajan Iyyappan & Giovanna Nascimento Scatolin & Zongliang Jiang & Timour Baslan & Amnon Koren & Dieter Egli, 2024. "DNA replication in early mammalian embryos is patterned, predisposing lamina-associated regions to fragility," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    7. Xinjun Li & Fan Feng & Hongxi Pu & Wai Yan Leung & Jie Liu, 2021. "scHiCTools: A computational toolbox for analyzing single-cell Hi-C data," PLOS Computational Biology, Public Library of Science, vol. 17(5), pages 1-14, May.
    8. Sarah B. Reiff & Andrew J. Schroeder & Koray Kırlı & Andrea Cosolo & Clara Bakker & Luisa Mercado & Soohyun Lee & Alexander D. Veit & Alexander K. Balashov & Carl Vitzthum & William Ronchetti & Kent M, 2022. "The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    9. Dunming Hua & Ming Gu & Xiao Zhang & Yanyi Du & Hangcheng Xie & Li Qi & Xiangjun Du & Zhidong Bai & Xiaopeng Zhu & Dechao Tian, 2024. "DiffDomain enables identification of structurally reorganized topologically associating domains," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    10. Judith H. I. Haarhuis & Robin H. Weide & Vincent A. Blomen & Koen D. Flach & Hans Teunissen & Laureen Willems & Thijn R. Brummelkamp & Benjamin D. Rowland & Elzo Wit, 2022. "A Mediator-cohesin axis controls heterochromatin domain formation," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    11. Da Lin & Weize Xu & Ping Hong & Chengchao Wu & Zhihui Zhang & Siheng Zhang & Lingyu Xing & Bing Yang & Wei Zhou & Qin Xiao & Jinyue Wang & Cong Wang & Yu He & Xi Chen & Xiaojian Cao & Jiangwei Man & A, 2022. "Decoding the spatial chromatin organization and dynamic epigenetic landscapes of macrophage cells during differentiation and immune activation," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
    12. Yufan Zhou & Tian Li & Lavanya Choppavarapu & Kun Fang & Shili Lin & Victor X. Jin, 2024. "Integration of scHi-C and scRNA-seq data defines distinct 3D-regulated and biological-context dependent cell subpopulations," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    13. Hua Yu & Zhen Sun & Tianyu Tan & Hongru Pan & Jing Zhao & Ling Zhang & Jiayu Chen & Anhua Lei & Yuqing Zhu & Lang Chen & Yuyan Xu & Yaxin Liu & Ming Chen & Jinghao Sheng & Zhengping Xu & Pengxu Qian &, 2021. "rRNA biogenesis regulates mouse 2C-like state by 3D structure reorganization of peri-nucleolar heterochromatin," Nature Communications, Nature, vol. 12(1), pages 1-21, December.

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