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

ABSTRACT:

Background

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.

Results

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-GD

SUBMITTER: Lee H 

PROVIDER: S-EPMC11927400 | biostudies-literature | 2025 Jan

REPOSITORIES: biostudies-literature