ArticleCommunications biology2020
Rice 3D chromatin structure correlates with sequence variation and meiotic recombination rate.
Article in Communications biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Haplotype-Resolved 3D Genomic Landscapes and Their Impacts on Agronomic Traits in Grapevine.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Replication timing uncovers a two-compartment nuclear architecture of interphase euchromatin.The Plant cell · 2026Article
- Domestication shaped the chromatin landscape of grain amaranth.Nature communications · 2025Article
- Identification of Rice LncRNAs and Their Roles in the Rice Blast Resistance Network Using Transcriptome and Translatome.Plants (Basel, Switzerland) · 2025Article
- Polymer-derived distance penalties improve chromatin interaction predictions from single-cell data across crop genomes.bioRxiv : the preprint server for biology · 2025Article
- Are complex traits underpinned by polygenic molecular traits? A reflection on the complexity of gene expression.Plant & cell physiology · 2025Review
- Topologically associating domains and the evolution of three-dimensional genome architecture in rice.The Plant journal : for cell and molecular biology · 2025Article
- Chromatin Topological Domains Associate With the Rapid Formation of Tandem Duplicates in Plants.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Comprehensive mapping and modelling of the rice regulome landscape unveils the regulatory architecture underlying complex traits.Nature communications · 2024Article
- Insight into chromatin compaction and spatial organization in rice interphase nuclei.Frontiers in plant science · 2024Article
- Unlocking the Secret to Higher Crop Yield: The Potential for Histone Modifications.Plants (Basel, Switzerland) · 2023Review
- MethBank 4.0: an updated database of DNA methylation across a variety of species.Nucleic acids research · 2023Article
- Elucidating the biology of transcription factor-DNA interaction for accurate identification of cis-regulatory elements.Current opinion in plant biology · 2022Review
- Plant biosynthetic gene clusters in the context of metabolic evolution.Natural product reports · 2022Review
- The 3D architecture of the pepper genome and its relationship to function and evolution.Nature communications · 2022Article
- Review
- Meiosis in crops: from genes to genomes.Journal of experimental botany · 2021Review
- Understanding 3D Genome Organization and Its Effect on Transcriptional Gene Regulation Under Environmental Stress in Plant: A Chromatin Perspective.Frontiers in cell and developmental biology · 2021Review
- The Formation of Bivalents and the Control of Plant Meiotic Recombination.Frontiers in plant science · 2021Review
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genomes of many eukaryotic species have a defined three-dimensional architecture critical for cellular processes. They are partitioned into topologically associated domains (TADs), defined as regions of high chromatin inter-connectivity. While TADs are not a prominent feature of A. thaliana genome organization, they have been reported for other plants including rice, maize, tomato and cotton and for which TAD formation appears to be linked to transcription and chromatin epigenetic status. Here we show that in the rice genome, sequence variation and meiotic recombination rate correlate with the 3D genome structure. TADs display increased SNP and SV density and higher recombination rate compared to inter-TAD regions. We associate the observed differences with the TAD epigenetic landscape, TE composition and an increased incidence of meiotic crossovers.
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