ArticleGenome biology2023
Cell-specific clock-controlled gene expression program regulates rhythmic fiber cell growth in cotton.
Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 53 citations in OpenAlex.
- Advances in single-cell and spatial multi-omics for plant development and stress responses.Plant diversity · 2026Review
- Integrating single-cell omic techniques to resolve the spatio-temporal complexity of arbuscular mycorrhizal symbiosis.Journal of experimental botany · 2026Review
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- Plant Peptides on the Rise: From Historical Insight to Future Applications.Plant biotechnology journal · 2026Review
- RNA-seq and ATAC-seq reveal candidate genes and regulatory networks underlying exogenous ABA-enhanced abiotic stress tolerance in Gossypium hirsutum.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Comprehensive insights into the development of arabidopsis trichomes by single-nucleus RNA-seq.BMC plant biology · 2026Article
- Integrated experimental and computational workflows for single-cell transcriptomics in plants.Plant methods · 2026Article
- Global atlas of enhancer-promoter interactome in cotton genome revealed by profiling RNA-RNA spatial interactions.Genome biology · 2026Article
- Comparative single-cell transcriptomic map reveals divergence in leaves between two cotton species at cell type resolution.Journal of advanced research · 2026Article
- Single-cell multi-omics data reveal heterogeneity in liver tissue microenvironment induced by hypertension.Molecular therapy. Nucleic acids · 2025Article
- Photoperiod and Circadian Regulation in Plants: A Review of Insights from In Vitro Studies.Biology · 2025Review
- Spatiotemporal methylome remodeling during fiber differentiation in Gossypium hirsutum.BMC genomics · 2025Article
- Transcriptional activation and repression in the plant circadian clock: Revisiting core oscillator feedback loops and output pathways.Plant communications · 2025Review
- Genetic dissection of lint percentage in an introgression population between Gossypium hirsutum and G. mustelinum.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Reversing anther thermotolerance by manipulating the cis-elements in the promoter of a high-temperature upregulated gene Casein Kinase I in upland cotton.Science China. Life sciences · 2025Article
- GhLPF1 Associated Network Is Involved with Cotton Lint Percentage Regulation Revealed by the Integrative Analysis of Spatial Transcriptome.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Orthologous marker groups reveal broad cell identity conservation across plant single-cell transcriptomes.Nature communications · 2025Article
- Using Callus as an Ex Vivo System for Chromatin Analysis.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Genome-wide identification and characterization of soybean GH9 endo-1,4-β-glucanases.Frontiers in plant science · 2025Article
- Harnessing Single-Cell and Spatial Transcriptomics for Crop Improvement.Plants (Basel, Switzerland) · 2024Review
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Authors and funding
17 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe epidermis of cotton ovule produces fibers, the most important natural cellulose source for the global textile industry. However, the molecular mechanism of fiber cell growth is still poorly understood.
resultsHere, we develop an optimized protoplasting method, and integrate single-cell RNA sequencing (scRNA-seq) and single-cell ATAC sequencing (scATAC-seq) to systematically characterize the cells of the outer integument of ovules from wild type and fuzzless/lintless (fl) cotton (Gossypium hirsutum). By jointly analyzing the scRNA-seq data from wildtype and fl, we identify five cell populations including the fiber cell type and construct the development trajectory for fiber lineage cells. Interestingly, by time-course diurnal transcriptomic analysis, we demonstrate that the primary growth of fiber cells is a highly regulated circadian rhythmic process. Moreover, we identify a small peptide GhRALF1 that circadian rhythmically controls fiber growth possibly through oscillating auxin signaling and proton pump activity in the plasma membrane. Combining with scATAC-seq, we further identify two cardinal cis-regulatory elements (CREs, TCP motif, and TCP-like motif) which are bound by the trans factors GhTCP14s to modulate the circadian rhythmic metabolism of mitochondria and protein translation through regulating approximately one third of genes that are highly expressed in fiber cells.
conclusionsWe uncover a fiber-specific circadian clock-controlled gene expression program in regulating fiber growth. This study unprecedentedly reveals a new route to improve fiber traits by engineering the circadian clock of fiber cells.
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