ArticleGenome biology2023
3D organization of regulatory elements for transcriptional regulation in Arabidopsis.
Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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22 citing papers in PubMed, 32 citations in OpenAlex.
- Occupancy-based mechanism is the chief mode of ROS1 function in preventing DNA hypermethylation.Nature plants · 2026Article
- The environmentally responsive plant epigenome: insights from jasmonate signaling.The New phytologist · 2026Review
- Centromere organization and epigenetic regulation in Aristolochia fimbriata.Genome biology · 2026Article
- Synthetic promoter design in plants: integration of computational and experimental approaches.Frontiers in plant science · 2026Review
- Genomic and epigenomic coordination maintains subgenome transcriptional balance in allotetraploidHorticulture research · 2026Article
- PKL mediates H3K4me2 modification and spatial gene congregation in chromatin regulation.Nucleic acids research · 2025Article
- Promoter Motif Profiling and Binding Site Distribution Analysis of Transcription Factors Predict Auto- and Cross-Regulatory Mechanisms inInternational journal of molecular sciences · 2025Article
- Epigenetic crop improvement: Integrating ENCODE strategies into horticultural breeding.Horticulture research · 2025Article
- A circadian morning complex modulates far-red light signaling in Arabidopsis.Nature communications · 2025Article
- A heat stress-responsive epigenome defines the dynamic 3D chromatin structure in Chinese cabbage.Plant physiology · 2025Article
- PRC1-Mediated H2Aub Loop Formation and Function in Arabidopsis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- TAC-C uncovers open chromatin interaction in crops and SPL-mediated photosynthesis regulation.Science advances · 2025Article
- Hi-GDT: A Hi-C-based 3D gene domain analysis tool for analyzing local chromatin contacts in plants.GigaScience · 2025Article
- Promoter capture Hi-C identifies promoter-related loops and fountain structures in Arabidopsis.Genome biology · 2024Article
- Epigenomic and 3D genomic mapping reveals developmental dynamics and subgenomic asymmetry of transcriptional regulatory architecture in allotetraploid cotton.Nature communications · 2024Article
- High-throughput capture of transcription factor-driven epigenome dynamics using PHILO ChIP-seq.Nucleic acids research · 2024Article
- A review of deep learning models for the prediction of chromatin interactions with DNA and epigenomic profiles.Briefings in bioinformatics · 2024Review
- Light control of three-dimensional chromatin organization in soybean.Plant biotechnology journal · 2024Article
- Genome organization and botanical diversity.The Plant cell · 2024Review
- Advances in the multimodal analysis of the 3D chromatin structure and gene regulation.Experimental & molecular medicine · 2024Review
Corrections and comments
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Authors and funding
15 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAlthough spatial organization of compartments and topologically associating domains at large scale is relatively well studied, the spatial organization of regulatory elements at fine scale is poorly understood in plants.
resultsHere we perform high-resolution chromatin interaction analysis using paired-end tag sequencing approach. We map chromatin interactions tethered with RNA polymerase II and associated with heterochromatic, transcriptionally active, and Polycomb-repressive histone modifications in Arabidopsis. Analysis of the regulatory repertoire shows that distal active cis-regulatory elements are linked to their target genes through long-range chromatin interactions with increased expression of the target genes, while poised cis-regulatory elements are linked to their target genes through long-range chromatin interactions with depressed expression of the target genes. Furthermore, we demonstrate that transcription factor MYC2 is critical for chromatin spatial organization, and propose that MYC2 occupancy and MYC2-mediated chromatin interactions coordinately facilitate transcription within the framework of 3D chromatin architecture. Analysis of functionally related gene-defined chromatin connectivity networks reveals that genes implicated in flowering-time control are functionally compartmentalized into separate subdomains via their spatial activity in the leaf or shoot apical meristem, linking active mark- or Polycomb-repressive mark-associated chromatin conformation to coordinated gene expression.
conclusionThe results reveal that the regulation of gene transcription in Arabidopsis is not only by linear juxtaposition, but also by long-range chromatin interactions. Our study uncovers the fine scale genome organization of Arabidopsis and the potential roles of such organization in orchestrating transcription and development.
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