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Integrating Hi-C and FISH data for modeling of the 3D organization of chromosomes

Author

Listed:
  • Ahmed Abbas

    (Tsinghua University)

  • Xuan He

    (Tsinghua University)

  • Jing Niu

    (Tsinghua University)

  • Bin Zhou

    (Tsinghua University)

  • Guangxiang Zhu

    (Tsinghua University)

  • Tszshan Ma

    (Tsinghua University)

  • Jiangpeikun Song

    (Tsinghua University)

  • Juntao Gao

    (Tsinghua University)

  • Michael Q. Zhang

    (Tsinghua University
    Tsinghua University
    the University of Texas at Dallas)

  • Jianyang Zeng

    (Tsinghua University
    Tsinghua University)

Abstract

The new advances in various experimental techniques that provide complementary information about the spatial conformations of chromosomes have inspired researchers to develop computational methods to fully exploit the merits of individual data sources and combine them to improve the modeling of chromosome structure. Here we propose GEM-FISH, a method for reconstructing the 3D models of chromosomes through systematically integrating both Hi-C and FISH data with the prior biophysical knowledge of a polymer model. Comprehensive tests on a set of chromosomes, for which both Hi-C and FISH data are available, demonstrate that GEM-FISH can outperform previous chromosome structure modeling methods and accurately capture the higher order spatial features of chromosome conformations. Moreover, our reconstructed 3D models of chromosomes revealed interesting patterns of spatial distributions of super-enhancers which can provide useful insights into understanding the functional roles of these super-enhancers in gene regulation.

Suggested Citation

  • Ahmed Abbas & Xuan He & Jing Niu & Bin Zhou & Guangxiang Zhu & Tszshan Ma & Jiangpeikun Song & Juntao Gao & Michael Q. Zhang & Jianyang Zeng, 2019. "Integrating Hi-C and FISH data for modeling of the 3D organization of chromosomes," Nature Communications, Nature, vol. 10(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-10005-6
    DOI: 10.1038/s41467-019-10005-6
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