ChIP-Hub: an Integrative Platform for Exploring Plant Regulome

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 > 10000 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 chromatin states based on comparative genomics. Taken together, the ChIP-Hub platform and the analysis results provide rich resources for deep exploration of plant ENCODE.