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Connecting high-resolution 3D chromatin organization with epigenomics

Author

Listed:
  • Fan Feng

    (University of Michigan)

  • Yuan Yao

    (University of Michigan)

  • Xue Qing David Wang

    (University of Southern California)

  • Xiaotian Zhang

    (University of Michigan)

  • Jie Liu

    (University of Michigan
    University of Michigan)

Abstract

The resolution of chromatin conformation capture technologies keeps increasing, and the recent nucleosome resolution chromatin contact maps allow us to explore how fine-scale 3D chromatin organization is related to epigenomic states in human cells. Using publicly available Micro-C datasets, we develop a deep learning model, CAESAR, to learn a mapping function from epigenomic features to 3D chromatin organization. The model accurately predicts fine-scale structures, such as short-range chromatin loops and stripes, that Hi-C fails to detect. With existing epigenomic datasets from ENCODE and Roadmap Epigenomics Project, we successfully impute high-resolution 3D chromatin contact maps for 91 human tissues and cell lines. In the imputed high-resolution contact maps, we identify the spatial interactions between genes and their experimentally validated regulatory elements, demonstrating CAESAR’s potential in coupling transcriptional regulation with 3D chromatin organization at high resolution.

Suggested Citation

  • Fan Feng & Yuan Yao & Xue Qing David Wang & Xiaotian Zhang & Jie Liu, 2022. "Connecting high-resolution 3D chromatin organization with epigenomics," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-29695-6
    DOI: 10.1038/s41467-022-29695-6
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    References listed on IDEAS

    as
    1. Shilu Zhang & Deborah Chasman & Sara Knaack & Sushmita Roy, 2019. "In silico prediction of high-resolution Hi-C interaction matrices," Nature Communications, Nature, vol. 10(1), pages 1-18, December.
    2. Yun Zhu & Zhao Chen & Kai Zhang & Mengchi Wang & David Medovoy & John W. Whitaker & Bo Ding & Nan Li & Lina Zheng & Wei Wang, 2016. "Constructing 3D interaction maps from 1D epigenomes," Nature Communications, Nature, vol. 7(1), pages 1-11, April.
    3. Yan Zhang & Lin An & Jie Xu & Bo Zhang & W. Jim Zheng & Ming Hu & Jijun Tang & Feng Yue, 2018. "Enhancing Hi-C data resolution with deep convolutional neural network HiCPlus," Nature Communications, Nature, vol. 9(1), pages 1-9, December.
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