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 ()
Additional contact information
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
References: View references in EconPapers View complete reference list from CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/s41467-025-59424-8 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-59424-8

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-025-59424-8

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().