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BL-Hi-C is an efficient and sensitive approach for capturing structural and regulatory chromatin interactions

Author

Listed:
  • Zhengyu Liang

    (Tsinghua University)

  • Guipeng Li

    (Tsinghua University
    Southern University of Science and Technology)

  • Zejun Wang

    (Tsinghua University)

  • Mohamed Nadhir Djekidel

    (Tsinghua University)

  • Yanjian Li

    (Tsinghua University)

  • Min-Ping Qian

    (Peking University)

  • Michael Q. Zhang

    (Tsinghua University
    The University of Texas)

  • Yang Chen

    (Tsinghua University
    Tsinghua University)

Abstract

In human cells, DNA is hierarchically organized and assembled with histones and DNA-binding proteins in three dimensions. Chromatin interactions play important roles in genome architecture and gene regulation, including robustness in the developmental stages and flexibility during the cell cycle. Here we propose in situ Hi-C method named Bridge Linker-Hi-C (BL-Hi-C) for capturing structural and regulatory chromatin interactions by restriction enzyme targeting and two-step proximity ligation. This method improves the sensitivity and specificity of active chromatin loop detection and can reveal the regulatory enhancer-promoter architecture better than conventional methods at a lower sequencing depth and with a simpler protocol. We demonstrate its utility with two well-studied developmental loci: the beta-globin and HOXC cluster regions.

Suggested Citation

  • Zhengyu Liang & Guipeng Li & Zejun Wang & Mohamed Nadhir Djekidel & Yanjian Li & Min-Ping Qian & Michael Q. Zhang & Yang Chen, 2017. "BL-Hi-C is an efficient and sensitive approach for capturing structural and regulatory chromatin interactions," Nature Communications, Nature, vol. 8(1), pages 1-7, December.
    • Handle: RePEc:nat:natcom:v:8:y:2017:i:1:d:10.1038_s41467-017-01754-3
    DOI: 10.1038/s41467-017-01754-3
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    Cited by:

    1. Jie Zhang & Gongcheng Hu & Yuli Lu & Huawei Ren & Yin Huang & Yulin Wen & Binrui Ji & Diyang Wang & Haidong Wang & Huisheng Liu & Ning Ma & Lingling Zhang & Guangjin Pan & Yibo Qu & Hua Wang & Wei Zha, 2024. "CTCF mutation at R567 causes developmental disorders via 3D genome rearrangement and abnormal neurodevelopment," Nature Communications, Nature, vol. 15(1), pages 1-21, December.

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