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The 4D nucleome project

Author

Listed:
  • Job Dekker

    (Program in Systems Biology, University of Massachusetts Medical School, Howard Hughes Medical Institute)

  • Andrew S. Belmont

    (University of Illinois)

  • Mitchell Guttman

    (California Institute of Technology)

  • Victor O. Leshyk

    (University of California San Diego)

  • John T. Lis

    (Cornell University)

  • Stavros Lomvardas

    (Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University)

  • Leonid A. Mirny

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

  • Clodagh C. O’Shea

    (Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies)

  • Peter J. Park

    (Harvard Medical School)

  • Bing Ren

    (Ludwig Institute for Cancer Research, Institute of Genomic Medicine, Moores Cancer Center, University of California San Diego)

  • Joan C. Ritland Politz

    (Basic Sciences, Fred Hutchinson Cancer Research Center)

  • Jay Shendure

    (University of Washington, Howard Hughes Medical Institute)

  • Sheng Zhong

    (University of California San Diego)

Abstract

The 4D Nucleome Network aims to develop and apply approaches to map the structure and dynamics of the human and mouse genomes in space and time with the goal of gaining deeper mechanistic insights into how the nucleus is organized and functions. The project will develop and benchmark experimental and computational approaches for measuring genome conformation and nuclear organization, and investigate how these contribute to gene regulation and other genome functions. Validated experimental technologies will be combined with biophysical approaches to generate quantitative models of spatial genome organization in different biological states, both in cell populations and in single cells.

Suggested Citation

  • Job Dekker & Andrew S. Belmont & Mitchell Guttman & Victor O. Leshyk & John T. Lis & Stavros Lomvardas & Leonid A. Mirny & Clodagh C. O’Shea & Peter J. Park & Bing Ren & Joan C. Ritland Politz & Jay S, 2017. "The 4D nucleome project," Nature, Nature, vol. 549(7671), pages 219-226, September.
    • Handle: RePEc:nat:nature:v:549:y:2017:i:7671:d:10.1038_nature23884
    DOI: 10.1038/nature23884
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    Cited by:

    1. Jingxuan Xu & Xiang Xu & Dandan Huang & Yawen Luo & Lin Lin & Xuemei Bai & Yang Zheng & Qian Yang & Yu Cheng & An Huang & Jingyi Shi & Xiaochen Bo & Jin Gu & Hebing Chen, 2024. "A comprehensive benchmarking with interpretation and operational guidance for the hierarchy of topologically associating domains," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    2. Zhongxuan Zhang & Xiaoxiao Rong & Tianjin Xie & Zehao Li & Haozhi Song & Shujun Zhen & Haifeng Wang & Jiahui Wu & Samie R. Jaffrey & Xing Li, 2024. "Fluorogenic CRISPR for genomic DNA imaging," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    3. Riccardo Calandrelli & Xingzhao Wen & John Lalith Charles Richard & Zhifei Luo & Tri C. Nguyen & Chien-Ju Chen & Zhijie Qi & Shuanghong Xue & Weizhong Chen & Zhangming Yan & Weixin Wu & Kathia Zaleta-, 2023. "Genome-wide analysis of the interplay between chromatin-associated RNA and 3D genome organization in human cells," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    4. 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.
    5. Ryan J. Geusz & Allen Wang & Dieter K. Lam & Nicholas K. Vinckier & Konstantinos-Dionysios Alysandratos & David A. Roberts & Jinzhao Wang & Samy Kefalopoulou & Araceli Ramirez & Yunjiang Qiu & Joshua , 2021. "Sequence logic at enhancers governs a dual mechanism of endodermal organ fate induction by FOXA pioneer factors," Nature Communications, Nature, vol. 12(1), pages 1-19, December.
    6. Haowen Zhang & Li Song & Xiaotao Wang & Haoyu Cheng & Chenfei Wang & Clifford A. Meyer & Tao Liu & Ming Tang & Srinivas Aluru & Feng Yue & X. Shirley Liu & Heng Li, 2021. "Fast alignment and preprocessing of chromatin profiles with Chromap," Nature Communications, Nature, vol. 12(1), pages 1-6, December.
    7. Jia Lu & Xiaoyi Cao & Sheng Zhong, 2018. "A likelihood approach to testing hypotheses on the co-evolution of epigenome and genome," PLOS Computational Biology, Public Library of Science, vol. 14(12), pages 1-28, December.
    8. Hao Wang & Jiaxin Yang & Yu Zhang & Jianliang Qian & Jianrong Wang, 2022. "Reconstruct high-resolution 3D genome structures for diverse cell-types using FLAMINGO," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    9. Hannah L. Harris & Huiya Gu & Moshe Olshansky & Ailun Wang & Irene Farabella & Yossi Eliaz & Achyuth Kalluchi & Akshay Krishna & Mozes Jacobs & Gesine Cauer & Melanie Pham & Suhas S. P. Rao & Olga Dud, 2023. "Chromatin alternates between A and B compartments at kilobase scale for subgenic organization," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    10. Andrea M. Chiariello & Alex Abraham & Simona Bianco & Andrea Esposito & Andrea Fontana & Francesca Vercellone & Mattia Conte & Mario Nicodemi, 2024. "Multiscale modelling of chromatin 4D organization in SARS-CoV-2 infected cells," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    11. 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.
    12. Jorine M. Eeftens & Manya Kapoor & Davide Michieletto & Clifford P. Brangwynne, 2021. "Polycomb condensates can promote epigenetic marks but are not required for sustained chromatin compaction," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    13. Dominik Beck & Honghui Cao & Feng Tian & Yizhou Huang & Miao Jiang & Han Zhao & Xiaolu Tai & Wenqian Xu & Hansen J. Kosasih & David J. Kealy & Weiye Zhao & Samuel J. Taylor & Timothy A. Couttas & Gaox, 2024. "PU.1 eviction at lymphocyte-specific chromatin domains mediates glucocorticoid response in acute lymphoblastic leukemia," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    14. Mayank N. K. Choudhary & Kara Quaid & Xiaoyun Xing & Heather Schmidt & Ting Wang, 2023. "Widespread contribution of transposable elements to the rewiring of mammalian 3D genomes," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    15. Abhijit Chakraborty & Jeffrey G. Wang & Ferhat Ay, 2022. "dcHiC detects differential compartments across multiple Hi-C datasets," Nature Communications, Nature, vol. 13(1), pages 1-21, December.

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