ChIP-Hub provides an integrative platform for exploring plant regulome

Liang-Yu Fu, Tao Zhu, Xinkai Zhou, Ranran Yu, Zhaohui He, Peijing Zhang, Zhigui Wu, Ming Chen, Kerstin Kaufmann () and Dijun Chen ()
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Liang-Yu Fu: Nanjing University
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

Nature Communications, 2022, vol. 13, issue 1, 1-15

Abstract: 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/ .

Date: 2022
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DOI: 10.1038/s41467-022-30770-1

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