IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v14y2023i1d10.1038_s41467-023-38922-7.html
   My bibliography  Save this article

Holocentromeres can consist of merely a few megabase-sized satellite arrays

Author

Listed:
  • Yi-Tzu Kuo

    (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben)

  • Amanda Souza Câmara

    (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben)

  • Veit Schubert

    (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben)

  • Pavel Neumann

    (Czech Academy of Sciences, Institute of Plant Molecular Biology)

  • Jiří Macas

    (Czech Academy of Sciences, Institute of Plant Molecular Biology)

  • Michael Melzer

    (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben)

  • Jianyong Chen

    (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben)

  • Jörg Fuchs

    (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben)

  • Simone Abel

    (Julius Kühn-Institute (JKI), Institute for Breeding Research on Horticultural Crops)

  • Evelyn Klocke

    (Julius Kühn-Institute (JKI), Institute for Breeding Research on Horticultural Crops)

  • Bruno Huettel

    (Max Planck Institute for Plant Breeding Research)

  • Axel Himmelbach

    (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben)

  • Dmitri Demidov

    (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben)

  • Frank Dunemann

    (Julius Kühn-Institute (JKI), Institute for Breeding Research on Horticultural Crops)

  • Martin Mascher

    (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben)

  • Takayoshi Ishii

    (Tottori University)

  • André Marques

    (Max Planck Institute for Plant Breeding Research)

  • Andreas Houben

    (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben)

Abstract

The centromere is the chromosome region where microtubules attach during cell division. In contrast to monocentric chromosomes with one centromere, holocentric species usually distribute hundreds of centromere units along the entire chromatid. We assembled the chromosome-scale reference genome and analyzed the holocentromere and (epi)genome organization of the lilioid Chionographis japonica. Remarkably, each of its holocentric chromatids consists of only 7 to 11 evenly spaced megabase-sized centromere-specific histone H3-positive units. These units contain satellite arrays of 23 and 28 bp-long monomers capable of forming palindromic structures. Like monocentric species, C. japonica forms clustered centromeres in chromocenters at interphase. In addition, the large-scale eu- and heterochromatin arrangement differs between C. japonica and other known holocentric species. Finally, using polymer simulations, we model the formation of prometaphase line-like holocentromeres from interphase centromere clusters. Our findings broaden the knowledge about centromere diversity, showing that holocentricity is not restricted to species with numerous and small centromere units.

Suggested Citation

  • Yi-Tzu Kuo & Amanda Souza Câmara & Veit Schubert & Pavel Neumann & Jiří Macas & Michael Melzer & Jianyong Chen & Jörg Fuchs & Simone Abel & Evelyn Klocke & Bruno Huettel & Axel Himmelbach & Dmitri Dem, 2023. "Holocentromeres can consist of merely a few megabase-sized satellite arrays," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-38922-7
    DOI: 10.1038/s41467-023-38922-7
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-023-38922-7
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-023-38922-7?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Peter Eastman & Jason Swails & John D Chodera & Robert T McGibbon & Yutong Zhao & Kyle A Beauchamp & Lee-Ping Wang & Andrew C Simmonett & Matthew P Harrigan & Chaya D Stern & Rafal P Wiewiora & Bernar, 2017. "OpenMM 7: Rapid development of high performance algorithms for molecular dynamics," PLOS Computational Biology, Public Library of Science, vol. 13(7), pages 1-17, July.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Yennifer Mata-Sucre & Marie Krátká & Ludmila Oliveira & Pavel Neumann & Jiří Macas & Veit Schubert & Bruno Huettel & Eduard Kejnovský & Andreas Houben & Andrea Pedrosa-Harand & Gustavo Souza & André M, 2024. "Repeat-based holocentromeres of the woodrush Luzula sylvatica reveal insights into the evolutionary transition to holocentricity," Nature Communications, Nature, vol. 15(1), pages 1-15, December.

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. repec:plo:pbio00:3000919 is not listed on IDEAS
    2. Qiwen Su-Tobon & Jiayi Fan & Michael Goldstein & Kevin Feeney & Hongyuan Ren & Patrick Autissier & Peiyi Wang & Yingzi Huang & Udayan Mohanty & Jia Niu, 2025. "CRISPR-Hybrid: A CRISPR-Mediated Intracellular Directed Evolution Platform for RNA Aptamers," Nature Communications, Nature, vol. 16(1), pages 1-13, December.
    3. Christian Hentrich & Mateusz Putyrski & Hanh Hanuschka & Waldemar Preis & Sarah-Jane Kellmann & Melissa Wich & Manuel Cavada & Sarah Hanselka & Victor S. Lelyveld & Francisco Ylera, 2024. "Engineered reversible inhibition of SpyCatcher reactivity enables rapid generation of bispecific antibodies," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    4. Sophie Dürauer & Hyun-Seo Kang & Christian Wiebeler & Yuka Machida & Dina S. Schnapka & Denitsa Yaneva & Christian Renz & Maximilian J. Götz & Pedro Weickert & Abigail C. Major & Aldwin S. Rahmanto & , 2025. "Allosteric activation of the SPRTN protease by ubiquitin maintains genome stability," Nature Communications, Nature, vol. 16(1), pages 1-17, December.
    5. Andreas Mardt & Tim Hempel & Cecilia Clementi & Frank Noé, 2022. "Deep learning to decompose macromolecules into independent Markovian domains," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    6. Cheng Shen & Yuqing Zhang & Wenwen Cui & Yimeng Zhao & Danqi Sheng & Xinyu Teng & Miaoqing Shao & Muneyoshi Ichikawa & Jin Wang & Motoyuki Hattori, 2023. "Structural insights into the allosteric inhibition of P2X4 receptors," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    7. Siran Tian & Hung Nguyen & Ziqing Ye & Silvi Rouskin & D. Thirumalai & Tatjana Trcek, 2025. "Controlling intermolecular base pairing in Drosophila germ granules by mRNA folding and its implications in fly development," Nature Communications, Nature, vol. 16(1), pages 1-22, December.
    8. Xiaorong Li & Xiaoxu Yang & Xiaoli Lu & Bingqian Lin & Yuanyuan Zhang & Bangdong Huang & Yutong Zhou & Jing Huang & Kun Wu & Qiang Zhou & Ximin Chi, 2025. "Structural basis for substrate recognition mechanism of human SLC26A7," Nature Communications, Nature, vol. 16(1), pages 1-10, December.
    9. Emilie Ma & Fadma Lakhal & Eleni Litsardaki & Myriam Ruault & Maxime Audin & Natacha Levrier & Emilie Navarro & Mickaël Garnier & Laurent Maloisel & Jordane Depagne & Clémentine Brocas & Aurelien Thur, 2025. "A large C-terminal Rad52 segment acts as a chaperone to Form and Stabilize Rad51 Filaments," Nature Communications, Nature, vol. 16(1), pages 1-18, December.
    10. F. P. Panei & P. Gkeka & M. Bonomi, 2024. "Identifying small-molecules binding sites in RNA conformational ensembles with SHAMAN," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    11. Bin Han & Kuang Yu, 2025. "Refining potential energy surface through dynamical properties via differentiable molecular simulation," Nature Communications, Nature, vol. 16(1), pages 1-12, December.
    12. Shana Bergman & Rosemary J. Cater & Ambrose Plante & Filippo Mancia & George Khelashvili, 2023. "Substrate binding-induced conformational transitions in the omega-3 fatty acid transporter MFSD2A," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    13. Kuang-Ting Ko & Frank Lennartz & David Mekhaiel & Bora Guloglu & Arianna Marini & Danielle J. Deuker & Carole A. Long & Matthijs M. Jore & Kazutoyo Miura & Sumi Biswas & Matthew K. Higgins, 2022. "Structure of the malaria vaccine candidate Pfs48/45 and its recognition by transmission blocking antibodies," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    14. Simon Alberti & Paolo Arosio & Robert B. Best & Steven Boeynaems & Danfeng Cai & Rosana Collepardo-Guevara & Gregory L. Dignon & Rumiana Dimova & Shana Elbaum-Garfinkle & Nicolas L. Fawzi & Monika Fux, 2025. "Current practices in the study of biomolecular condensates: a community comment," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
    15. Baris E. Ugur & Michael A. Webb, 2025. "Nuclear quantum effects in molecular liquids across chemical space," Nature Communications, Nature, vol. 16(1), pages 1-11, December.
    16. Hongjun Bai & Eric Lewitus & Yifan Li & Paul V. Thomas & Michelle Zemil & Mélanie Merbah & Caroline E. Peterson & Thujitha Thuraisamy & Phyllis A. Rees & Agnes Hajduczki & Vincent Dussupt & Bonnie Sli, 2024. "Contemporary HIV-1 consensus Env with AI-assisted redesigned hypervariable loops promote antibody binding," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    17. Taro Yasuma & Hajime Fujimoto & Corina N. D’Alessandro-Gabazza & Masaaki Toda & Mei Uemura & Kota Nishihama & Atsuro Takeshita & Valeria Fridman D’Alessandro & Tomohito Okano & Yuko Okano & Atsushi To, 2025. "Microbiota-derived corisin accelerates kidney fibrosis by promoting cellular aging," Nature Communications, Nature, vol. 16(1), pages 1-29, December.
    18. Do Hoon Kwon & Feng Zhang & Brett A. McCray & Shasha Feng & Meha Kumar & Jeremy M. Sullivan & Wonpil Im & Charlotte J. Sumner & Seok-Yong Lee, 2023. "TRPV4-Rho GTPase complex structures reveal mechanisms of gating and disease," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    19. Xiaotong Diao & Qinghong Shang & Mengqi Guo & Yubin Huang & Meina Zhang & Xiaoyu Chen & Yinping Liang & Xiangnan Sun & Fan Zhou & Jingjing Zhuang & Shuang-Jiang Liu & Christoph F. A. Vogel & Fraydoon , 2025. "Structural basis for the ligand-dependent activation of heterodimeric AHR-ARNT complex," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
    20. Ritaban Halder & Daniel A. Nissley & Ian Sitarik & Yang Jiang & Yiyun Rao & Quyen V. Vu & Mai Suan Li & Justin Pritchard & Edward P. O’Brien, 2023. "How soluble misfolded proteins bypass chaperones at the molecular level," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    21. Giacomo Janson & Gilberto Valdes-Garcia & Lim Heo & Michael Feig, 2023. "Direct generation of protein conformational ensembles via machine learning," Nature Communications, Nature, vol. 14(1), pages 1-14, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-38922-7. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.