ArticleNature communications2025
48-Hour and 24-Hour Time-lapse Single-nucleus Transcriptomics Reveal Cell-type specific Circadian Rhythms in Arabidopsis.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Time- and space-resolved transcriptional regulation in Arabidopsis thaliana.Plant biology (Stuttgart, Germany) · 2026Article
- Time after time: a quarter century of progress in plant circadian biology.Npj biological timing and sleep · 2026Review
- Early birds and night owls: natural variation of circadian traits in plants.Journal of experimental botany · 2026Review
- Rhythmic Mechanisms Governing CAM Photosynthesis inInternational journal of molecular sciences · 2026Article
- Unveiling the early defense response dynamics in grapevines against Plasmopara viticola by single-cell transcriptomics.Genome biology · 2026Article
- GEAR: an integrated atlas of gene expression dynamics in Arabidopsis thaliana.Nucleic acids research · 2026Article
- FX-Cell: a method for single-cell RNA sequencing on difficult-to-digest and cryopreserved plant samples.Nature methods · 2025Article
- High resolution diel transcriptomes of autotetraploid potato reveal expression and sequence conservation among rhythmic genes.BMC genomics · 2025Article
- Genome-Wide Identification of the AP2/ERF Gene Family and Functional Analysis ofPlants (Basel, Switzerland) · 2025Article
- 48-Hour and 24-Hour Time-lapse Single-nucleus Transcriptomics Reveal Cell-type specific Circadian Rhythms in Arabidopsis.Nature communications · 2025Article
- Stable and dynamic gene expression patterns over diurnal and developmental timescales in Arabidopsis thaliana.The New phytologist · 2025Article
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Authors and funding
12 authors.
Funding
Abstract
Functional circadian clock is critical to the adaptation and survival of organisms. In land plants, the comprehensive profiling of circadian gene expression at the single-cell level is largely unknown partly due to the challenges in obtaining precisely-timed single cells embedded within cell walls. To bridge this gap, we employ time-lapse single-nucleus RNA sequencing (snRNA-seq) on Arabidopsis seedlings collected over a 48-hour window at 4-hour intervals, as well as over a 24-hour day at 2-hour intervals, yielding a total of over 77,142 and 130,000 nuclei. Here, we find that four cell clusters in the shoot share a coherent rhythm, while around 3000 genes display cell-type specific rhythmic expression. Our analysis indicates that genes encoding circadian regulators oscillate in multiple cell types, and the majority of them are well-documented core clock genes, suggesting the snRNA-seq circadian data could be used to identify more clock components oscillating in a cell-autonomous way. We identify ABF1 as a circadian regulator, whose overexpression and shortens the circadian period. Our data provides a comprehensive resource for plant circadian rhythmicity at the single-cell level (hosted at https://zhailab.bio.sustech.edu.cn/sc_circadian ).
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