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A high-resolution map of the three-dimensional chromatin interactome in human cells

Author

Listed:
  • Fulai Jin

    (Ludwig Institute for Cancer Research, 9500 Gilman Drive)

  • Yan Li

    (Ludwig Institute for Cancer Research, 9500 Gilman Drive)

  • Jesse R. Dixon

    (Ludwig Institute for Cancer Research, 9500 Gilman Drive
    UCSD Medical Scientist Training Program, University of California, San Diego, School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA)

  • Siddarth Selvaraj

    (Ludwig Institute for Cancer Research, 9500 Gilman Drive
    UCSD Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA)

  • Zhen Ye

    (Ludwig Institute for Cancer Research, 9500 Gilman Drive)

  • Ah Young Lee

    (Ludwig Institute for Cancer Research, 9500 Gilman Drive)

  • Chia-An Yen

    (Ludwig Institute for Cancer Research, 9500 Gilman Drive)

  • Anthony D. Schmitt

    (Ludwig Institute for Cancer Research, 9500 Gilman Drive
    UCSD Biomedical Sciences Graduate Program, University of California, San Diego, School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA)

  • Celso A. Espinoza

    (Ludwig Institute for Cancer Research, 9500 Gilman Drive)

  • Bing Ren

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

Abstract

A novel approach to analyse high-depth Hi-C data provides a comprehensive chromatin interaction map at approximately 5–10 kb resolution in human fibroblasts; this reveals that TNF-α-responsive enhancers are already in contact with target promoters before signalling and that this chromatin looping is a strong predictor of gene induction.

Suggested Citation

  • Fulai Jin & Yan Li & Jesse R. Dixon & Siddarth Selvaraj & Zhen Ye & Ah Young Lee & Chia-An Yen & Anthony D. Schmitt & Celso A. Espinoza & Bing Ren, 2013. "A high-resolution map of the three-dimensional chromatin interactome in human cells," Nature, Nature, vol. 503(7475), pages 290-294, November.
    • Handle: RePEc:nat:nature:v:503:y:2013:i:7475:d:10.1038_nature12644
    DOI: 10.1038/nature12644
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    Citations

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    Cited by:

    1. Claudia Fierro & Veronica Gatti & Veronica Banca & Sara Domenico & Stefano Scalera & Giacomo Corleone & Maurizio Fanciulli & Francesca Nicola & Alessandro Mauriello & Manuela Montanaro & George A. Cal, 2023. "The long non-coding RNA NEAT1 is a ΔNp63 target gene modulating epidermal differentiation," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    2. Zhaohui Qin & Ben Li & Karen N. Conneely & Hao Wu & Ming Hu & Deepak Ayyala & Yongseok Park & Victor X. Jin & Fangyuan Zhang & Han Zhang & Li Li & Shili Lin, 2016. "Statistical Challenges in Analyzing Methylation and Long-Range Chromosomal Interaction Data," Statistics in Biosciences, Springer;International Chinese Statistical Association, vol. 8(2), pages 284-309, October.
    3. 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.
    4. Hye Ji Cha & Özgün Uyan & Yan Kai & Tianxin Liu & Qian Zhu & Zuzana Tothova & Giovanni A. Botten & Jian Xu & Guo-Cheng Yuan & Job Dekker & Stuart H. Orkin, 2021. "Inner nuclear protein Matrin-3 coordinates cell differentiation by stabilizing chromatin architecture," Nature Communications, Nature, vol. 12(1), pages 1-19, December.
    5. Zhang Qi & Xu Zheng & Lai Yutong, 2021. "An Empirical Bayes approach for the identification of long-range chromosomal interaction from Hi-C data," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 20(1), pages 1-15, February.
    6. David Santiago-Algarra & Charbel Souaid & Himanshu Singh & Lan T. M. Dao & Saadat Hussain & Alejandra Medina-Rivera & Lucia Ramirez-Navarro & Jaime A. Castro-Mondragon & Nori Sadouni & Guillaume Charb, 2021. "Epromoters function as a hub to recruit key transcription factors required for the inflammatory response," Nature Communications, Nature, vol. 12(1), pages 1-18, December.
    7. 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.

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