PlantCADB: A comprehensive plant chromatin accessibility database

Abstract

Chromatin accessibility landscapes are essential for detecting regulatory elements, illustrating the corresponding regulatory networks, and, ultimately, understanding the molecular bases underlying key biological processes. With the advancement of sequencing technologies, a large volume of chromatin accessibility data has been accumulated and integrated in humans and other mammals. These data have greatly advanced the study of disease pathogenesis, cancer survival prognosis, and tissue development. To advance the understanding of molecular mechanisms regulating plant key traits and biological processes, we developed a comprehensive plant chromatin accessibility database (PlantCADB, https://bioinfor.nefu.edu.cn/PlantCADB/) from 649 samples of 37 species. Among these samples, 159 are abiotic stress-related (including heat, cold, drought, salt, etc.), 232 are development-related and 376 are tissue-specific. Overall, 18,339,426 accessible chromatin regions (ACRs) were compiled. These ACRs were annotated with genomic information, associated genes, transcription factors footprint, motif, and SNPs. Additionally, PlantCADB provides various tools to visualize ACRs and corresponding annotations. It thus forms an integrated, annotated, and analyzed plant-related chromatin accessibility information which can aid to better understand genetic regulatory networks underlying development, important traits, stress adaptions, and evolution.