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bioRxiv · 10.1101/2023.12.09.570919

A Day in the Life of Arabidopsis: 24-Hour Time-lapse Single-nucleus Transcriptomics Reveal Cell-type specific Circadian Rhythms

Qin, Y.·Liu, Z.·Gao, S.·Long, Y.·Zhu, X.·Liu, B.·Gao, Y.·Xie, Q.·Nohales, M. A.·Xu, X.·Zhai, J.
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Abstract

Functional circadian clock is fundamental 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 from plant cells embedded within cell walls. To bridge this gap, we employed single-nucleus RNA sequencing (snRNA-seq) on twelve seedling samples collected at 2-hour intervals over a 24-hour day in Arabidopsis, yielding a total of over 130,000 nuclei. From this data, we found that three cell clusters in the shoot share a coherent rhythm, while more than 3,000 genes display cell-type specific rhythmic expression. Only 19 genes are oscillating in more than ten different cell types, and the majority of them are well-documented core oscillators, suggesting the snRNA-seq circadian data could be used to identify key circadian regulators in a broad range of plant systems. Our data provides the first comprehensive resource for plant circadian rhythms at the single-cell level (hosted at https://zhailab.bio.sustech.edu.cn/sc_circadian).

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Qin, Y., Liu, Z., Gao, S., Long, Y., Zhu, X., Liu, B., Gao, Y., Xie, Q., Nohales, M. A., Xu, X., Zhai, J.. 2023-12-10. A Day in the Life of Arabidopsis: 24-Hour Time-lapse Single-nucleus Transcriptomics Reveal Cell-type specific Circadian Rhythms. https://doi.org/10.1101/2023.12.09.570919

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