ArticleGenome research2016
Genome-wide analysis of chromatin packing in Arabidopsis thaliana at single-gene resolution.
Article in Genome research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 115 papers.
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Who cites it
115 citing papers in PubMed.
- A deep learning model captures position-specific effects of plant regulatory sequences and suggests genes under complex regulation.Plant physiology · 2026Article
- EMF2 deficiency disrupts epigenetic and chromatin organization landscapes, blocking root regeneration competence in Arabidopsis.The New phytologist · 2026Article
- 3D Chromatin Architecture Provides Insights Into Leaf Trait Variation Among Pear Species.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Profiling the transcriptional regulatory network reveals putative shared regulatory elements within homoeologs in polyploid Brassica napus.Genome biology · 2026Article
- Replication timing uncovers a two-compartment nuclear architecture of interphase euchromatin.The Plant cell · 2026Article
- Centromere organization and epigenetic regulation in Aristolochia fimbriata.Genome biology · 2026Article
- Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications.Chemical reviews · 2026Review
- Vegetative to generative1 (Vgt1) is an enhancer affecting flowering time and jasmonate signaling in maize by promoting the expression of Zea mays Related to APETALA 2.7.Plant physiology · 2025Article
- A haplotype-resolved chromatin landscape connects cis-regulatory variants to trait variation in Citrus.BMC genomics · 2025Article
- Plants repress ROS1 expression to attenuate heat-induced transposon burst.Nature plants · 2025Article
- PRC1-Mediated H2Aub Loop Formation and Function in Arabidopsis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Epigenetic state and gene expression remain stable after CRISPR/Cas-mediated chromosomal inversions.The New phytologist · 2025Article
- Dynamic changes in 3D chromatin structure during male gametogenesis in Arabidopsis thaliana.Genome biology · 2025Article
- Hi-GDT: A Hi-C-based 3D gene domain analysis tool for analyzing local chromatin contacts in plants.GigaScience · 2025Article
- Widespread 3D genome reorganization precedes programmed DNA rearrangement inbioRxiv : the preprint server for biology · 2025Article
- Article
- Promoter capture Hi-C identifies promoter-related loops and fountain structures in Arabidopsis.Genome biology · 2024Article
- Brassinosteroid signaling represses ZINC FINGER PROTEIN11 to regulate ovule development in Arabidopsis.The Plant cell · 2024Article
- Widespread position-dependent transcriptional regulatory sequences in plants.Nature genetics · 2024Article
- Light control of three-dimensional chromatin organization in soybean.Plant biotechnology journal · 2024Article
55 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The three-dimensional packing of the genome plays an important role in regulating gene expression. We have used Hi-C, a genome-wide chromatin conformation capture (3C) method, to analyze Arabidopsis thaliana chromosomes dissected into subkilobase segments, which is required for gene-level resolution in this species with a gene-dense genome. We found that the repressive H3K27me3 histone mark is overrepresented in the promoter regions of genes that are in conformational linkage over long distances. In line with the globally dispersed distribution of RNA polymerase II in A. thaliana nuclear space, actively transcribed genes do not show a strong tendency to associate with each other. In general, there are often contacts between 5' and 3' ends of genes, forming local chromatin loops. Such self-loop structures of genes are more likely to occur in more highly expressed genes, although they can also be found in silent genes. Silent genes with local chromatin loops are highly enriched for the histone variant H3.3 at their 5' and 3' ends but depleted of repressive marks such as heterochromatic histone modifications and DNA methylation in flanking regions. Our results suggest that, different from animals, a major theme of genome folding in A. thaliana is the formation of structural units that correspond to gene bodies.
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