ArticleGenome research2015
Genome-wide analysis of local chromatin packing in Arabidopsis thaliana.
Article in Genome research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 158 papers, 1 of them a synthesis that pooled it.
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Who cites it
158 citing papers in PubMed, 1 synthesis or guideline pooled it.
- ChIP-Hub provides an integrative platform for exploring plant regulome.Nature communications · 2022Pooled it
- TADs, CGVs, and compartmentalization in genomes: Providing a new way for crop domestication and improvement.Journal of integrative plant biology · 2026Review
- 3D Chromatin Architecture Provides Insights Into Leaf Trait Variation Among Pear Species.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- 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
- Centromere organization and epigenetic regulation in Aristolochia fimbriata.Genome biology · 2026Article
- Allele-specific chromatin dynamics underpin heterosis and shoot development in hybrid poplar 'Nanlin895'.Plant molecular biology · 2026Article
- Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications.Chemical reviews · 2026Review
- Comparative genomics analyses reveal genomic variation and evolutionary adaptation in Dendrobium orchids.Nature communications · 2025Article
- Dynamic 3D chromatin organization and epigenetic regulation of gene expression in peanut nodules.Journal of integrative plant biology · 2025Article
- A nearly complete haplotype-phased genome assembly of nerve plant (Horticulture research · 2025Article
- Genome Mountaineering: Expanding Horizons of the 3D Genome for the Intrepid Evolutionary Adventurer.Genome biology and evolution · 2025Review
- Are complex traits underpinned by polygenic molecular traits? A reflection on the complexity of gene expression.Plant & cell physiology · 2025Review
- Telomere-to-telomere, gap-free genome of mung bean (Horticulture research · 2025Article
- A chromosome-scale genome assembly and epigenomic profiling reveal temperature-dependent histone methylation in iridoid biosynthesis regulation inHorticulture research · 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
- Promoter capture Hi-C identifies promoter-related loops and fountain structures in Arabidopsis.Genome biology · 2024Article
- Cohesin distribution alone predicts chromatin organization in yeast via conserved-current loop extrusion.Genome biology · 2024Article
- 3D chromatin maps of a brown alga reveal U/V sex chromosome spatial organization.Nature communications · 2024Article
98 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The spatial arrangement of interphase chromosomes in the nucleus is important for gene expression and genome function in animals and in plants. The recently developed Hi-C technology is an efficacious method to investigate genome packing. Here we present a detailed Hi-C map of the three-dimensional genome organization of the plant Arabidopsis thaliana. We find that local chromatin packing differs from the patterns seen in animals, with kilobasepair-sized segments that have much higher intrachromosome interaction rates than neighboring regions, representing a dominant local structural feature of genome conformation in A. thaliana. These regions, which appear as positive strips on two-dimensional representations of chromatin interaction, are enriched in epigenetic marks H3K27me3, H3.1, and H3.3. We also identify more than 400 insulator-like regions. Furthermore, although topologically associating domains (TADs), which are prominent in animals, are not an obvious feature of A. thaliana genome packing, we found more than 1000 regions that have properties of TAD boundaries, and a similar number of regions analogous to the interior of TADs. The insulator-like, TAD-boundary-like, and TAD-interior-like regions are each enriched for distinct epigenetic marks and are each correlated with different gene expression levels. We conclude that epigenetic modifications, gene density, and transcriptional activity combine to shape the local packing of the A. thaliana nuclear genome.
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