ArticleNucleic acids research2023
Accessible gene borders establish a core structural unit for chromatin architecture in Arabidopsis.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed, 18 citations in OpenAlex.
- Deep Learning for Deciphering the Plant Cis-Regulatory Code.Plants (Basel, Switzerland) · 2026Review
- TADs, CGVs, and compartmentalization in genomes: Providing a new way for crop domestication and improvement.Journal of integrative plant biology · 2026Review
- TONSOKU prevents the formation of large tandem duplications and restrains ATR-WEE1 checkpoint activation.Nature communications · 2026Article
- Replication timing uncovers a two-compartment nuclear architecture of interphase euchromatin.The Plant cell · 2026Article
- Are complex traits underpinned by polygenic molecular traits? A reflection on the complexity of gene expression.Plant & cell physiology · 2025Review
- Topologically associating domains and the evolution of three-dimensional genome architecture in rice.The Plant journal : for cell and molecular biology · 2025Article
- Hi-GDT: A Hi-C-based 3D gene domain analysis tool for analyzing local chromatin contacts in plants.GigaScience · 2025Article
- 3D chromatin maps of a brown alga reveal U/V sex chromosome spatial organization.Nature communications · 2024Article
- Mutations of PDS5 genes enhance TAD-like domain formation Arabidopsis thaliana.Nature communications · 2024Article
- Widespread position-dependent transcriptional regulatory sequences in plants.Nature genetics · 2024Article
- A fine-scale Arabidopsis chromatin landscape reveals chromatin conformation-associated transcriptional dynamics.Nature communications · 2024Article
- Differences in transcription initiation directionality underlie distinctions between plants and animals in chromatin modification patterns at genes and cis-regulatory elements.G3 (Bethesda, Md.) · 2024Article
- Differences in transcription initiation directionality underlie distinctions between plants and animals in chromatin modification patterns at genes and cis-regulatory elements.bioRxiv : the preprint server for biology · 2023Article
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Authors and funding
2 authors at 1 institution in 1 country.
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Abstract
Three-dimensional (3D) chromatin structure is linked to transcriptional regulation in multicellular eukaryotes including plants. Taking advantage of high-resolution Hi-C (high-throughput chromatin conformation capture), we detected a small structural unit with 3D chromatin architecture in the Arabidopsis genome, which lacks topologically associating domains, and also in the genomes of tomato, maize, and Marchantia polymorpha. The 3D folding domain unit was usually established around an individual gene and was dependent on chromatin accessibility at the transcription start site (TSS) and transcription end site (TES). We also observed larger contact domains containing two or more neighboring genes, which were dependent on accessible border regions. Binding of transcription factors to accessible TSS/TES regions formed these gene domains. We successfully simulated these Hi-C contact maps via computational modeling using chromatin accessibility as input. Our results demonstrate that gene domains establish basic 3D chromatin architecture units that likely contribute to higher-order 3D genome folding in plants.
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