48-Hour and 24-Hour Time-lapse Single-nucleus Transcriptomics Reveal Cell-type specific Circadian Rhythms in Arabidopsis

Yuwei Qin, Zhijian Liu, Shiqi Gao, Carlos Martínez-Vasallo, Yanping Long, Xinlong Zhu, Bin Liu, Ya Gao, Xiaodong Xu, Maria A. Nohales (), Qiguang Xie () and Jixian Zhai ()
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Yuwei Qin: Southern University of Science and Technology
Zhijian Liu: Northeast Normal University
Shiqi Gao: Henan University
Carlos Martínez-Vasallo: Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia
Yanping Long: Southern University of Science and Technology
Xinlong Zhu: Southern University of Science and Technology
Bin Liu: Chinese Academy of Agricultural Sciences
Ya Gao: Henan University
Xiaodong Xu: Henan University
Maria A. Nohales: Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia
Qiguang Xie: Henan University
Jixian Zhai: Southern University of Science and Technology

Nature Communications, 2025, vol. 16, issue 1, 1-14

Abstract: 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 ).

Date: 2025
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DOI: 10.1038/s41467-025-59424-8

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