Hi-GDT: A Hi-C-based 3D gene domain analysis tool for analyzing local chromatin contacts in Arabidopsis

However, we lack effective tools to identify these contact domains and examine their structural dynamics. Here, we developed the Hi-C-based 3D Gene Domain analysis Tool (Hi-GDT) to identify fine-scale local chromatin contact domains in the model plant Arabidopsis, with a particular focus on gene borders. We report that Hi-GDT successfully identifies local contact domains, including single-gene and multigene domains, with high reproducibility. Hi-GDT can also be used to discover local contact domains that are differentially organized in association with differences in gene expression between tissue types or in response to environmental stimuli. Overall, Hi-GDT is a valuable tool for identifying genes regulated by dynamic 3D conformational changes, expanding our understanding of the structural and functional relevance of local 3D chromatin organization in plants.