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GigaScience, Jan 06 2025, 14 giaf020 | https://doi.org/10.1093/gigascience/giaf020
Hi-GDT: A Hi-C-based 3D gene domain analysis tool for analyzing local chromatin contacts in plants
Hongwoo Lee 1 and Pil Joon Seo 1,2,*
1Department of Chemistry, Seoul National University, Seoul 08826, Korea
2Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea
∗Correspondence: Pil Joon Seo
1Department of Chemistry, Seoul National University, Seoul 08826, Korea
2Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea
∗Correspondence: Pil Joon Seo
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-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.
Conclusions: 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.
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-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.
Conclusions: 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.
논문정보
- Research article
- 2025년 01월 (BRIC 등록일 2025-03-24)
- 국내 연구진
- 생명과학 > 식물학
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