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

文献类型： 外文期刊

作者： Qin, Yuwei 1 ; Liu, Zhijian 2 ; Gao, Shiqi 3 ; Martinez-Vasallo, Carlos 4 ; Long, Yanping 1 ; Zhu, Xinlong 1 ; Liu, Bin 5 ; Gao, Ya 3 ; Xu, Xiaodong 3 ; Nohales, Maria A. 4 ; Xie, Qiguang 3 ; Zhai, Jixian 1 ;

作者机构： 1.Southern Univ Sci & Technol, Inst Plant & Food Sci, Sch Life Sci, Dept Biol,Shenzhen Key Lab Plant Genet Engn & Mol, Shenzhen, Peoples R China

2.Northeast Normal Univ, Key Lab Mol Epigenet Minist Educ, Changchun, Peoples R China

3.Henan Univ, Sch Life Sci, State Key Lab Crop Stress Adaptat & Improvement, Kaifeng, Peoples R China

4.Univ Politecn Valencia, Consejo Super Invest Cient, Inst Biol Mol & Celular Plantas IBMCP, Valencia, Spain

5.Chinese Acad Agr Sci, Inst Crop Sci, State Key Lab Crop Gene Resources & Breeding, Beijing, Peoples R China

期刊名称：NATURE COMMUNICATIONS （ 影响因子：15.7； 五年影响因子：17.2 ）

ISSN：

年卷期： 2025 年 16 卷 1 期

页码：

收录情况： SCI

摘要： 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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