Lee Hongwoo, Seo Pil Joon
Department of Chemistry, Seoul National University, Seoul 08826, Korea.
Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea.
Gigascience. 2025 Jan 6;14. doi: 10.1093/gigascience/giaf020.
Three-dimensional (3D) chromatin organization is emerging as a key factor in gene regulation in eukaryotes. Recent studies using high-resolution Hi-C analysis have explored fine-scale local chromatin contact domains in plants, as exemplified by the basic contact domains established at accessible gene border regions in Arabidopsis (Arabidopsis thaliana). However, we lack effective tools to identify these contact domains and examine their structural dynamics.
We developed the Hi-C-based 3D Gene Domain analysis Tool (Hi-GDT) to identify fine-scale local chromatin contact domains in plants, with a particular focus on gene borders. 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, genotypes, or in response to environmental stimuli.
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. Hi-GDT is publicly available at https://github.com/CDL-HongwooLee/Hi-GDT.
三维（3D）染色质组织正逐渐成为真核生物基因调控中的关键因素。最近使用高分辨率Hi-C分析的研究已经探索了植物中精细尺度的局部染色质接触结构域，例如拟南芥中可及基因边界区域建立的基本接触结构域。然而，我们缺乏有效的工具来识别这些接触结构域并研究其结构动态。
我们开发了基于Hi-C的3D基因结构域分析工具（Hi-GDT），以识别植物中精细尺度的局部染色质接触结构域，特别关注基因边界。Hi-GDT成功地识别了局部接触结构域，包括单基因和多基因结构域，具有很高的可重复性。Hi-GDT还可用于发现与组织类型、基因型之间的基因表达差异或对环境刺激的反应相关的差异组织的局部接触结构域。
Hi-GDT是一种用于识别受动态3D构象变化调控的基因的有价值工具，扩展了我们对植物局部3D染色质组织的结构和功能相关性的理解。Hi-GDT可在https://github.com/CDL-HongwooLee/Hi-GDT上公开获取。
