ArticleNature communications2024
A fine-scale Arabidopsis chromatin landscape reveals chromatin conformation-associated transcriptional dynamics.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 18 citations in OpenAlex.
- Intrinsically disordered regions restrain genomic targeting of RNA and histone demethylases in mammals and plants.Nature genetics · 2026Article
- Molecular mechanism of cold acclimation regulating freezing tolerance in Prunus mume.Plant physiology · 2026Article
- Application of deep learning in crop research: From genomics to phenomics.The plant genome · 2026Review
- NanoLoop: A Deep Learning Framework Leveraging Nanopore Sequencing for Chromatin Loop Prediction.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Long Noncoding RNAs as Emerging Regulators of Seed Development, Germination, and Senescence.International journal of molecular sciences · 2025Review
- BMI1s interact with condensin complexes to regulate chromatin 3D structure and gene expression inaBIOTECH · 2025Article
- A haplotype-resolved reference genome for Eucalyptus grandis.G3 (Bethesda, Md.) · 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
- Mutations of PDS5 genes enhance TAD-like domain formation Arabidopsis thaliana.Nature communications · 2024Article
- Connecting high-resolution 3D chromatin maps with cell division and cell differentiation at the root apical meristem.Plant cell reports · 2024Article
- Exploring plant-microbe interactions in adapting to abiotic stress under climate change: a review.Frontiers in plant science · 2024Review
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Authors and funding
13 authors at 4 institutions in 3 countries.
Funding
Abstract
Plants, as sessile organisms, deploy transcriptional dynamics for adapting to extreme growth conditions such as cold stress. Emerging evidence suggests that chromatin architecture contributes to transcriptional regulation. However, the relationship between chromatin architectural dynamics and transcriptional reprogramming in response to cold stress remains unclear. Here, we apply a chemical-crosslinking assisted proximity capture (CAP-C) method to elucidate the fine-scale chromatin landscape, revealing chromatin interactions within gene bodies closely associated with RNA polymerase II (Pol II) densities across initiation, pausing, and termination sites. We observe dynamic changes in chromatin interactions alongside Pol II activity alterations during cold stress, suggesting local chromatin dynamics may regulate Pol II activity. Notably, cold stress does not affect large-scale chromatin conformations. We further identify a comprehensive promoter-promoter interaction (PPI) network across the genome, potentially facilitating co-regulation of gene expression in response to cold stress. Our study deepens the understanding of chromatin conformation-associated gene regulation in plant response to cold.
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Registered trials
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.