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

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Article in GigaScience, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

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1citing papers in PubMed

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1 citing paper in PubMed.

Hi-GDT: A Hi-C-based 3D gene domain analysis tool for analyzing local chromatin contacts in plants.GigaScience · 2025
Article

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5 · Who and what money

Authors and funding

2 authors.

Hongwoo LeeDepartment of Chemistry, Seoul National University, Seoul 08826, Korea.ORCID 0000-0002-9339-2757

Pil Joon SeoDepartment of Chemistry, Seoul National University, Seoul 08826, Korea.ORCID 0000-0002-5499-3138

Funding

Basic Research Laboratory NRF-2022R1A4A3024451Basic Science Research RS-2025-00517108National Research Foundation of Korea

6 · The paper itself

Abstract

backgroundThree-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.

resultsWe 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.

conclusionsHi-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.

Indexed as

ArabidopsisChromatinSoftwareGene Expression Regulation, PlantChromatinArabidopsisfine-scale contact domaingene domaingene domain analysis toolHi-C

Identifiers

PMID40117178

DOI10.1093/gigascience/giaf020

PMCPMC11927400

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LicenceCC BY

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.