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Topologically associating domains are stable units of replication-timing regulation

Author

Listed:
  • Benjamin D. Pope

    (319 Stadium Drive, Florida State University)

  • Tyrone Ryba

    (5800 Bay Shore Road, New College of Florida)

  • Vishnu Dileep

    (319 Stadium Drive, Florida State University)

  • Feng Yue

    (School of Medicine, The Pennsylvania State University
    Bioinformatics and Genomics Program, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park)

  • Weisheng Wu

    (Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park)

  • Olgert Denas

    (Emory University, O. Wayne Rollins Research Center, 1510 Clifton Road NE, Atlanta, Georgia 30322, USA)

  • Daniel L. Vera

    (319 Stadium Drive, Florida State University)

  • Yanli Wang

    (Bioinformatics and Genomics Program, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park)

  • R. Scott Hansen

    (University of Washington)

  • Theresa K. Canfield

    (University of Washington)

  • Robert E. Thurman

    (University of Washington)

  • Yong Cheng

    (Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA)

  • Günhan Gülsoy

    (Computer and Information Sciences and Engineering, University of Florida)

  • Jonathan H. Dennis

    (319 Stadium Drive, Florida State University)

  • Michael P. Snyder

    (Stanford University, 300 Pasteur Drive, MC-5477 Stanford, California 94305, USA)

  • John A. Stamatoyannopoulos

    (University of Washington)

  • James Taylor

    (Emory University, O. Wayne Rollins Research Center, 1510 Clifton Road NE, Atlanta, Georgia 30322, USA
    Present address: Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA.)

  • Ross C. Hardison

    (Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park)

  • Tamer Kahveci

    (Computer and Information Sciences and Engineering, University of Florida)

  • Bing Ren

    (Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA)

  • David M. Gilbert

    (319 Stadium Drive, Florida State University)

Abstract

A study of DNA replication timing in mouse and human cells reveals that replication domains (domains of the genome which replicate at the same time) share a correlation with topologically associating domains; these results reconcile cell-type-specific sub-nuclear compartmentalization with developmentally stable chromosome domains and offer a unified model for large scale chromosome structure and function.

Suggested Citation

  • Benjamin D. Pope & Tyrone Ryba & Vishnu Dileep & Feng Yue & Weisheng Wu & Olgert Denas & Daniel L. Vera & Yanli Wang & R. Scott Hansen & Theresa K. Canfield & Robert E. Thurman & Yong Cheng & Günhan G, 2014. "Topologically associating domains are stable units of replication-timing regulation," Nature, Nature, vol. 515(7527), pages 402-405, November.
    • Handle: RePEc:nat:nature:v:515:y:2014:i:7527:d:10.1038_nature13986
    DOI: 10.1038/nature13986
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    Cited by:

    1. Silvia Peripolli & Leticia Meneguello & Chiara Perrod & Tanya Singh & Harshil Patel & Sazia T. Rahman & Koshiro Kiso & Peter Thorpe & Vincenzo Calvanese & Cosetta Bertoli & Robertus A. M. de Bruin, 2024. "Oncogenic c-Myc induces replication stress by increasing cohesins chromatin occupancy in a CTCF-dependent manner," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    2. Khalid H. Bhat & Saurabh Priyadarshi & Sarah Naiyer & Xinyan Qu & Hammad Farooq & Eden Kleiman & Jeffery Xu & Xue Lei & Jose F. Cantillo & Robert Wuerffel & Nicole Baumgarth & Jie Liang & Ann J. Feene, 2023. "An Igh distal enhancer modulates antigen receptor diversity by determining locus conformation," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    3. Michelle Dietzen & Haoran Zhai & Olivia Lucas & Oriol Pich & Christopher Barrington & Wei-Ting Lu & Sophia Ward & Yanping Guo & Robert E. Hynds & Simone Zaccaria & Charles Swanton & Nicholas McGranaha, 2024. "Replication timing alterations are associated with mutation acquisition during breast and lung cancer evolution," Nature Communications, Nature, vol. 15(1), pages 1-23, December.
    4. Koon-Kiu Yan & Shaoke Lou & Mark Gerstein, 2017. "MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutions," PLOS Computational Biology, Public Library of Science, vol. 13(7), pages 1-22, July.
    5. 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.
    6. Benjamin Walker & Dane Taylor & Josh Lawrimore & Caitlin Hult & David Adalsteinsson & Kerry Bloom & M Gregory Forest, 2019. "Transient crosslinking kinetics optimize gene cluster interactions," PLOS Computational Biology, Public Library of Science, vol. 15(8), pages 1-28, August.
    7. Lorenzo Corazzi & Vivien S. Ionasz & Sergej Andrejev & Li-Chin Wang & Athanasios Vouzas & Marco Giaisi & Giulia Di Muzio & Boyu Ding & Anna J. M. Marx & Jonas Henkenjohann & Michael M. Allers & David , 2024. "Linear interaction between replication and transcription shapes DNA break dynamics at recurrent DNA break Clusters," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    8. David E. Torres & H. Martin Kramer & Vittorio Tracanna & Gabriel L. Fiorin & David E. Cook & Michael F. Seidl & Bart P. H. J. Thomma, 2024. "Implications of the three-dimensional chromatin organization for genome evolution in a fungal plant pathogen," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    9. Cuifang Liu & Juan Yu & Aoqun Song & Min Wang & Jiansen Hu & Ping Chen & Jicheng Zhao & Guohong Li, 2023. "Histone H1 facilitates restoration of H3K27me3 during DNA replication by chromatin compaction," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    10. Cristiana Bersaglieri & Jelena Kresoja-Rakic & Shivani Gupta & Dominik Bär & Rostyslav Kuzyakiv & Martina Panatta & Raffaella Santoro, 2022. "Genome-wide maps of nucleolus interactions reveal distinct layers of repressive chromatin domains," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    11. Thais Ealo & Victor Sanchez-Gaya & Patricia Respuela & María Muñoz-San Martín & Elva Martin-Batista & Endika Haro & Alvaro Rada-Iglesias, 2024. "Cooperative insulation of regulatory domains by CTCF-dependent physical insulation and promoter competition," Nature Communications, Nature, vol. 15(1), pages 1-22, December.
    12. Stefano Gnan & Joseph M. Josephides & Xia Wu & Manuela Spagnuolo & Dalila Saulebekova & Mylène Bohec & Marie Dumont & Laura G. Baudrin & Daniele Fachinetti & Sylvain Baulande & Chun-Long Chen, 2022. "Kronos scRT: a uniform framework for single-cell replication timing analysis," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    13. Nimrod Rappoport & Elad Chomsky & Takashi Nagano & Charlie Seibert & Yaniv Lubling & Yael Baran & Aviezer Lifshitz & Wing Leung & Zohar Mukamel & Ron Shamir & Peter Fraser & Amos Tanay, 2023. "Single cell Hi-C identifies plastic chromosome conformations underlying the gastrulation enhancer landscape," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    14. Alon Diament & Tamir Tuller, 2015. "Improving 3D Genome Reconstructions Using Orthologous and Functional Constraints," PLOS Computational Biology, Public Library of Science, vol. 11(5), pages 1-22, May.
    15. Li-Hsin Chang & Sourav Ghosh & Andrea Papale & Jennifer M. Luppino & Mélanie Miranda & Vincent Piras & Jéril Degrouard & Joanne Edouard & Mallory Poncelet & Nathan Lecouvreur & Sébastien Bloyer & Amél, 2023. "Multi-feature clustering of CTCF binding creates robustness for loop extrusion blocking and Topologically Associating Domain boundaries," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    16. Ofir Shukron & David Holcman, 2017. "Transient chromatin properties revealed by polymer models and stochastic simulations constructed from Chromosomal Capture data," PLOS Computational Biology, Public Library of Science, vol. 13(4), pages 1-20, April.
    17. Daniel Malzl & Mihaela Peycheva & Ali Rahjouei & Stefano Gnan & Kyle N. Klein & Mariia Nazarova & Ursula E. Schoeberl & David M. Gilbert & Sara C. B. Buonomo & Michela Virgilio & Tobias Neumann & Rush, 2023. "RIF1 regulates early replication timing in murine B cells," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    18. Sora Yoon & Aditi Chandra & Golnaz Vahedi, 2022. "Stripenn detects architectural stripes from chromatin conformation data using computer vision," Nature Communications, Nature, vol. 13(1), pages 1-14, December.

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