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ChIP-Hub provides an integrative platform for exploring plant regulome

Author

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  • Liang-Yu Fu

    (Nanjing University
    Humboldt-Universität zu Berlin)

  • Tao Zhu

    (Nanjing University)

  • Xinkai Zhou

    (Nanjing University)

  • Ranran Yu

    (Nanjing University)

  • Zhaohui He

    (Nanjing University)

  • Peijing Zhang

    (Zhejiang University)

  • Zhigui Wu

    (Nanjing University)

  • Ming Chen

    (Zhejiang University)

  • Kerstin Kaufmann

    (Humboldt-Universität zu Berlin)

  • Dijun Chen

    (Nanjing University)

Abstract

Plant genomes encode a complex and evolutionary diverse regulatory grammar that forms the basis for most life on earth. A wealth of regulome and epigenome data have been generated in various plant species, but no common, standardized resource is available so far for biologists. Here, we present ChIP-Hub, an integrative web-based platform in the ENCODE standards that bundles >10,000 publicly available datasets reanalyzed from >40 plant species, allowing visualization and meta-analysis. We manually curate the datasets through assessing ~540 original publications and comprehensively evaluate their data quality. As a proof of concept, we extensively survey the co-association of different regulators and construct a hierarchical regulatory network under a broad developmental context. Furthermore, we show how our annotation allows to investigate the dynamic activity of tissue-specific regulatory elements (promoters and enhancers) and their underlying sequence grammar. Finally, we analyze the function and conservation of tissue-specific promoters, enhancers and chromatin states using comparative genomics approaches. Taken together, the ChIP-Hub platform and the analysis results provide rich resources for deep exploration of plant ENCODE. ChIP-Hub is available at https://biobigdata.nju.edu.cn/ChIPHub/ .

Suggested Citation

  • Liang-Yu Fu & Tao Zhu & Xinkai Zhou & Ranran Yu & Zhaohui He & Peijing Zhang & Zhigui Wu & Ming Chen & Kerstin Kaufmann & Dijun Chen, 2022. "ChIP-Hub provides an integrative platform for exploring plant regulome," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
  • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-30770-1
    DOI: 10.1038/s41467-022-30770-1
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    References listed on IDEAS

    as
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    2. Ashton S. Holub & Sarah G. Choudury & Ekaterina P. Andrianova & Courtney E. Dresden & Ricardo Urquidi Camacho & Igor B. Zhulin & Aman Y. Husbands, 2024. "START domains generate paralog-specific regulons from a single network architecture," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
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