ArticleGenome biology2022
Dynamic 3D genome architecture of cotton fiber reveals subgenome-coordinated chromatin topology for 4-staged single-cell differentiation.
Article in Genome biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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30 citing papers in PubMed, 49 citations in OpenAlex.
- Bivalent chromatin states and epigenetic priming in cotton: the role of H3K4me3 and H3K27me3 in cold stress memory and resilience.Epigenetics & chromatin · 2026Review
- 3D Chromatin Architecture Provides Insights Into Leaf Trait Variation Among Pear Species.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- PlantCTCIP: Chromatin Interaction Prediction Using Convolutional Neural Network and Transformer in Plants.Plant biotechnology journal · 2026Article
- Chromatin Topology Reconfiguration Orchestrates Thermotolerant Male Fertility via GhAL5 in Cotton.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Allele-specific chromatin dynamics underpin heterosis and shoot development in hybrid poplar 'Nanlin895'.Plant molecular biology · 2026Article
- Loss of multilevel 3D genome organization during breast cancer progression.Genome research · 2026Article
- Global atlas of enhancer-promoter interactome in cotton genome revealed by profiling RNA-RNA spatial interactions.Genome biology · 2026Article
- Genomic and epigenomic coordination maintains subgenome transcriptional balance in allotetraploidHorticulture research · 2026Article
- The ApWRKY26/ApERF4-ApMYB2 module regulates anthocyanin accumulation for the seasonal leaf color transition inHorticulture research · 2026Article
- A heat stress-responsive epigenome defines the dynamic 3D chromatin structure in Chinese cabbage.Plant physiology · 2025Article
- Epigenetics in the modern era of crop improvements.Science China. Life sciences · 2025Review
- Cotton transposon-related variome reveals roles of transposon-related variations in modern cotton cultivation.Journal of advanced research · 2025Article
- Topologically associating domains and the evolution of three-dimensional genome architecture in rice.The Plant journal : for cell and molecular biology · 2025Article
- Uncovering topologically associating domains from three-dimensional genome maps with TADGATE.Nucleic acids research · 2025Article
- Hi-GDT: A Hi-C-based 3D gene domain analysis tool for analyzing local chromatin contacts in plants.GigaScience · 2025Article
- Epigenomic and 3D genomic mapping reveals developmental dynamics and subgenomic asymmetry of transcriptional regulatory architecture in allotetraploid cotton.Nature communications · 2024Article
- Drought response revealed by chromatin organization variation and transcriptional regulation in cotton.BMC biology · 2024Article
- BL-Hi-C reveals the 3D genome structure ofHorticulture research · 2024Article
- High-quality Gossypium hirsutum and Gossypium barbadense genome assemblies reveal the landscape and evolution of centromeres.Plant communications · 2024Article
- Genomic insights into CKX genes: key players in cotton fibre development and abiotic stress responses.PeerJ · 2024Article
Corrections and comments
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Authors and funding
11 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDespite remarkable advances in our knowledge of epigenetically mediated transcriptional programming of cell differentiation in plants, little is known about chromatin topology and its functional implications in this process.
resultsTo interrogate its significance, we establish the dynamic three-dimensional (3D) genome architecture of the allotetraploid cotton fiber, representing a typical single cell undergoing staged development in plants. We show that the subgenome-relayed switching of the chromatin compartment from active to inactive is coupled with the silencing of developmentally repressed genes, pinpointing subgenome-coordinated contribution to fiber development. We identify 10,571 topologically associating domain-like (TAD-like) structures, of which 25.6% are specifically organized in different stages and 75.23% are subject to partition or fusion between two subgenomes. Notably, dissolution of intricate TAD-like structure cliques showing long-range interactions represents a prominent characteristic at the later developmental stage. Dynamic chromatin loops are found to mediate the rewiring of gene regulatory networks that exhibit a significant difference between the two subgenomes, implicating expression bias of homologous genes.
conclusionsThis study sheds light on the spatial-temporal asymmetric chromatin structures of two subgenomes in the cotton fiber and offers a new insight into the regulatory orchestration of cell differentiation in plants.
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