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A comprehensive benchmarking with interpretation and operational guidance for the hierarchy of topologically associating domains

Author

Listed:
  • Jingxuan Xu

    (Peking University Cancer Hospital & Institute)

  • Xiang Xu

    (Academy of Military Medical Science)

  • Dandan Huang

    (Peking University Shougang Hospital
    Peking University Health Science Center)

  • Yawen Luo

    (Academy of Military Medical Science)

  • Lin Lin

    (Academy of Military Medical Science
    Northeast Normal University)

  • Xuemei Bai

    (Academy of Military Medical Science)

  • Yang Zheng

    (Academy of Military Medical Science)

  • Qian Yang

    (Academy of Military Medical Science)

  • Yu Cheng

    (Peking University Cancer Hospital & Institute)

  • An Huang

    (Peking University Cancer Hospital & Institute)

  • Jingyi Shi

    (Peking University Cancer Hospital & Institute)

  • Xiaochen Bo

    (Academy of Military Medical Science)

  • Jin Gu

    (Peking University Cancer Hospital & Institute
    Peking University Shougang Hospital
    Peking University Health Science Center
    Peking University)

  • Hebing Chen

    (Academy of Military Medical Science)

Abstract

Topologically associating domains (TADs), megabase-scale features of chromatin spatial architecture, are organized in a domain-within-domain TAD hierarchy. Within TADs, the inner and smaller subTADs not only manifest cell-to-cell variability, but also precisely regulate transcription and differentiation. Although over 20 TAD callers are able to detect TAD, their usability in biomedicine is confined by a disagreement of outputs and a limit in understanding TAD hierarchy. We compare 13 computational tools across various conditions and develop a metric to evaluate the similarity of TAD hierarchy. Although outputs of TAD hierarchy at each level vary among callers, data resolutions, sequencing depths, and matrices normalization, they are more consistent when they have a higher similarity of larger TADs. We present comprehensive benchmarking of TAD hierarchy callers and operational guidance to researchers of life science researchers. Moreover, by simulating the mixing of different types of cells, we confirm that TAD hierarchy is generated not simply from stacking Hi-C heatmaps of heterogeneous cells. Finally, we propose an air conditioner model to decipher the role of TAD hierarchy in transcription.

Suggested Citation

  • 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.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-48593-7
    DOI: 10.1038/s41467-024-48593-7
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    References listed on IDEAS

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