ArticleNature communications2024
Mapping nucleosome-resolution chromatin organization and enhancer-promoter loops in plants using Micro-C-XL.
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 25 papers.
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25 citing papers in PubMed, 36 citations in OpenAlex.
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- BandHiC: a memory-efficient and user-friendly Python package for organizing and analyzing Hi-C matrices down to sub-kilobase resolution.BMC genomics · 2026Article
- TONSOKU prevents the formation of large tandem duplications and restrains ATR-WEE1 checkpoint activation.Nature communications · 2026Article
- Centromere organization and epigenetic regulation in Aristolochia fimbriata.Genome biology · 2026Article
- Multiple redundant mechanisms account for the majority of gene silencing downstream of DNA methylation.bioRxiv : the preprint server for biology · 2026Article
- Deciphering the 3D genome organization across species from Hi-C data.Nucleic acids research · 2026Article
- A low-input Micro-C protocol for high-resolution 3D genome mapping.Biology methods & protocols · 2026Article
- Immune signaling as a determinant of cellular identity and tissue function.Frontiers in immunology · 2026Review
- Novel genome editing approaches to manipulate apical meristem activity for crop yield.Frontiers in plant science · 2026Review
- Single-molecule views of chromatin accessibility and structure during photomorphogenesis.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Decades' progress and prospects on maize functional genomics and molecular breeding.Science China. Life sciences · 2025Review
- The evolutionary foundations of transcriptional regulation in animals.Nature reviews. Genetics · 2025Review
- Three-dimensional genome architecture connects chromatin structure and function in a major wheat pathogen.BMC biology · 2025Article
- A heat stress-responsive epigenome defines the dynamic 3D chromatin structure in Chinese cabbage.Plant physiology · 2025Article
- Microrchidia ATPases and DNA 6mA demethylase ALKBH1 act antagonistically on PRC2 to control chromatin structure and stress tolerance.Nature plants · 2025Article
- ISDH-seq: a robust methodology for profiling and characterization of open chromatin.Plant biotechnology journal · 2025Article
- Article
- Topologically associating domains and the evolution of three-dimensional genome architecture in rice.The Plant journal : for cell and molecular biology · 2025Article
- Hi-GDT: A Hi-C-based 3D gene domain analysis tool for analyzing local chromatin contacts in plants.GigaScience · 2025Article
- Mapping of chromatin architecture and enhancer-promoter interactions in the cochlea.Frontiers in molecular biosciences · 2025Article
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Authors and funding
10 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Although chromatin organizations in plants have been dissected at the scales of compartments and topologically associating domain (TAD)-like domains, there remains a gap in resolving fine-scale structures. Here, we use Micro-C-XL, a high-throughput chromosome conformation capture (Hi-C)-based technology that involves micrococcal nuclease (instead of restriction enzymes) and long cross-linkers, to dissect single nucleosome-resolution chromatin organization in Arabidopsis. Insulation analysis reveals more than 14,000 boundaries, which mostly include chromatin accessibility, epigenetic modifications, and transcription factors. Micro-C-XL reveals associations between RNA Pols and local chromatin organizations, suggesting that gene transcription substantially contributes to the establishment of local chromatin domains. By perturbing Pol II both genetically and chemically at the gene level, we confirm its function in regulating chromatin organization. Visible loops and stripes are assigned to super-enhancers and their targeted genes, thus providing direct insights for the identification and mechanistic analysis of distal CREs and their working modes in plants. We further investigate possible factors regulating these chromatin loops. Subsequently, we expand Micro-C-XL to soybean and rice. In summary, we use Micro-C-XL for analyses of plants, which reveal fine-scale chromatin organization and enhancer-promoter loops and provide insights regarding three-dimensional genomes in plants.
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