ArticleGenome biology2024
Promoter capture Hi-C identifies promoter-related loops and fountain structures in Arabidopsis.
Article in Genome biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Genetic diversity, GWAS, and candidate genes identification for plant architecture traits in maize (Zea mays L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Extrusion fountains are hallmarks of chromosome organization emerging upon zygotic genome activation.Nature communications · 2026Article
- Deciphering the 3D genome organization across species from Hi-C data.Nucleic acids research · 2026Article
- Novel genome editing approaches to manipulate apical meristem activity for crop yield.Frontiers in plant science · 2026Review
- PRC1-Mediated H2Aub Loop Formation and Function in Arabidopsis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- An efficient hairy root system for validation of CRISPR/Cas system activities in cotton.Functional & integrative genomics · 2025Article
- Promoter capture Hi-C identifies promoter-related loops and fountain structures in Arabidopsis.Genome biology · 2024Article
- ChIP-MS in Plant Systems: Mapping the H3K27ac Proteome During the Greening Process.Physiologia plantarumArticle
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundPromoters serve as key elements in the regulation of gene transcription. In mammals, loop interactions between promoters and enhancers increase the complexity of the promoter-based regulatory networks. However, the identification of enhancer-promoter or promoter-related loops in Arabidopsis remains incomplete.
resultsHere, we use promoter capture Hi-C to identify promoter-related loops in Arabidopsis, which shows that gene body, proximal promoter, and intergenic regions can interact with promoters, potentially functioning as distal regulatory elements or enhancers. We find that promoter-related loops mainly repress gene transcription and are associated with ordered chromatin structures, such as topologically associating domains and fountains-chromatin structures not previously identified in Arabidopsis. Cohesin binds to the center of fountains and is involved in their formation. Moreover, fountain strength is positively correlated with the number of promoter-related loops, and the maintenance of these loops is linked to H3K4me3. In atxr3 mutants, which lack the major H3K4me3 methyltransferases in Arabidopsis, the number of promoter-related loops at fountains is reduced, leading to upregulation of fountain-regulated genes.
conclusionsWe identify promoter-related loops associated with ordered chromatin structures and reveal the molecular mechanisms involved in fountain formation and maintenance.
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