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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： Yuwei Qin;Zhijian Liu;Shiqi Gao;Carlos Martínez-Vasallo;Yanping Long;Xinlong Zhu;Bin Liu;Ya Gao;Xiaodong Xu;Maria A. Nohales;Qiguang Xie;Jixian Zhai

作者机构：

期刊名称： Nature Communications

ISSN： 2041-1723

年卷期： 2025 年 16 卷 1 期

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收录情况： SCIE（2025版）

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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