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

[EN] 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 wa...

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Authors: Qin, Yuwei, Liu, Zhijian, Gao, Shiqi, Martínez-Vasallo, Carlos, Long, Yanping, Zhu, Xinlong, Liu, Bin, Gao, Ya, Xu, Xiaodong, Xie, Qiguang, Zhai, Jixian, Nohales, Maria A.
Format: article
Publication Date:2025
Country:España
Institution:Universitat Politècnica de València (UPV)
Repository:RiuNet. Repositorio Institucional de la Universitat Politécnica de Valéncia
Language:English
OAI Identifier:oai:riunet.upv.es:10251/221973
Online Access:https://riunet.upv.es/handle/10251/221973
Access Level:Open access
Keyword:Time-lapse single-nucleus RNA sequencing (snRNA-seq)
Cell types
Circadian regulators
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dc.title.none.fl_str_mv 48-Hour and 24-Hour Time-lapse Single-nucleus Transcriptomics Reveal Cell-type specific Circadian Rhythms in Arabidopsis
title 48-Hour and 24-Hour Time-lapse Single-nucleus Transcriptomics Reveal Cell-type specific Circadian Rhythms in Arabidopsis
spellingShingle 48-Hour and 24-Hour Time-lapse Single-nucleus Transcriptomics Reveal Cell-type specific Circadian Rhythms in Arabidopsis
Qin, Yuwei
Time-lapse single-nucleus RNA sequencing (snRNA-seq)
Cell types
Circadian regulators
title_short 48-Hour and 24-Hour Time-lapse Single-nucleus Transcriptomics Reveal Cell-type specific Circadian Rhythms in Arabidopsis
title_full 48-Hour and 24-Hour Time-lapse Single-nucleus Transcriptomics Reveal Cell-type specific Circadian Rhythms in Arabidopsis
title_fullStr 48-Hour and 24-Hour Time-lapse Single-nucleus Transcriptomics Reveal Cell-type specific Circadian Rhythms in Arabidopsis
title_full_unstemmed 48-Hour and 24-Hour Time-lapse Single-nucleus Transcriptomics Reveal Cell-type specific Circadian Rhythms in Arabidopsis
title_sort 48-Hour and 24-Hour Time-lapse Single-nucleus Transcriptomics Reveal Cell-type specific Circadian Rhythms in Arabidopsis
dc.creator.none.fl_str_mv Qin, Yuwei
Liu, Zhijian
Gao, Shiqi
Martínez-Vasallo, Carlos
Long, Yanping
Zhu, Xinlong
Liu, Bin
Gao, Ya
Xu, Xiaodong
Xie, Qiguang
Zhai, Jixian
Nohales, Maria A.
author Qin, Yuwei
author_facet Qin, Yuwei
Liu, Zhijian
Gao, Shiqi
Martínez-Vasallo, Carlos
Long, Yanping
Zhu, Xinlong
Liu, Bin
Gao, Ya
Xu, Xiaodong
Xie, Qiguang
Zhai, Jixian
Nohales, Maria A.
author_role author
author2 Liu, Zhijian
Gao, Shiqi
Martínez-Vasallo, Carlos
Long, Yanping
Zhu, Xinlong
Liu, Bin
Gao, Ya
Xu, Xiaodong
Xie, Qiguang
Zhai, Jixian
Nohales, Maria A.
author2_role author
author
author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Generalitat Valenciana
Government of Guangdong Province
Agencia Estatal de Investigación
Shanxi Scholarship Council of China
National Natural Science Foundation of China
Department of Education of Guangdong Province
Repositorio Institucional de la Universitat Politècnica de València Riunet
dc.subject.none.fl_str_mv Time-lapse single-nucleus RNA sequencing (snRNA-seq)
Cell types
Circadian regulators
topic Time-lapse single-nucleus RNA sequencing (snRNA-seq)
Cell types
Circadian regulators
description [EN] 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).
publishDate 2025
dc.date.none.fl_str_mv 2025
2025-05-05
dc.type.none.fl_str_mv journal article
http://purl.org/coar/resource_type/c_6501
VoR
http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv https://riunet.upv.es/handle/10251/221973
url https://riunet.upv.es/handle/10251/221973
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.relation.none.fl_str_mv Agencia Estatal de Investigación http://dx.doi.org/10.13039/501100011033 Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020 PID2020-119491GA-I00 CARACTERIZACION DE UNA RED REGULATORIA DEL RELOJ CIRCADIANO Y SU RECONFIGURACION EN RESPUESTA A DEFICIT DE AGUA
National Natural Science Foundation of China https://doi.org/10.13039/501100001809 31670285
National Natural Science Foundation of China https://doi.org/10.13039/501100001809 U1904202
National Natural Science Foundation of China https://doi.org/10.13039/501100001809 32325031
National Natural Science Foundation of China https://doi.org/10.13039/501100001809 32470601
National Natural Science Foundation of China https://doi.org/10.13039/501100001809 32300479
National Natural Science Foundation of China https://doi.org/10.13039/501100001809 32170259
Generalitat Valenciana https://doi.org/10.13039/501100003359 CIDEGENT%2F2020%2F037
Generalitat Valenciana https://doi.org/10.13039/501100003359 CIACIF%2F2021%2F329
Department of Education of Guangdong Province https://doi.org/10.13039/501100010226 2022KTSCX115
Shanxi Scholarship Council of China https://doi.org/10.13039/501100003398 ZDSYS20230626091659010
Government of Guangdong Province Government of Guangdong Province 2016ZT06S172
Government of Guangdong Province Government of Guangdong Province 2023ZD04073
Government of Guangdong Province Government of Guangdong Province 2023A1515011997
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
Reconocimiento - No comercial - Sin obra derivada (by-nc-nd)
http://creativecommons.org/licenses/by-nc-nd/4.0/
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
Reconocimiento - No comercial - Sin obra derivada (by-nc-nd)
http://creativecommons.org/licenses/by-nc-nd/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Nature Publishing Group
publisher.none.fl_str_mv Nature Publishing Group
dc.source.none.fl_str_mv reponame:RiuNet. Repositorio Institucional de la Universitat Politécnica de Valéncia
instname:Universitat Politècnica de València (UPV)
instname_str Universitat Politècnica de València (UPV)
reponame_str RiuNet. Repositorio Institucional de la Universitat Politécnica de Valéncia
collection RiuNet. Repositorio Institucional de la Universitat Politécnica de Valéncia
repository.name.fl_str_mv
repository.mail.fl_str_mv
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spelling 48-Hour and 24-Hour Time-lapse Single-nucleus Transcriptomics Reveal Cell-type specific Circadian Rhythms in ArabidopsisQin, YuweiLiu, ZhijianGao, ShiqiMartínez-Vasallo, CarlosLong, YanpingZhu, XinlongLiu, BinGao, YaXu, XiaodongXie, QiguangZhai, JixianNohales, Maria A.Time-lapse single-nucleus RNA sequencing (snRNA-seq)Cell typesCircadian regulators[EN] 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).The group of J.Z. is supported by the Biological Breeding-National Science and Technology Major Project (2023ZD04073), National Natural Science Foundation of China (32325031, 32470601), the Program for Guangdong Introducing Innovative and Entrepreneurial Teams (2016ZT06S172); Y.L. is supported by the National Natural Science Foundation of China (32300479), Natural Science Foundation of the Higher Education Institutions of Guangdong Province, China (2022KTSCX115) and Natural Science Foundation of Guangdong Province of China (2023A1515011997); and the National Natural Science Foundation of China to Q.X. (32170259, 31670285) and X.X. (U1904202, 32170275); Central Plains Science and Technology Innovation Leadership Talent Program to X.X. (234200510023); Z.L. is supported by the Fundamental Research Fund for Central Universities (2412023YQ005); M.A.N. is supported by MCIN/AEI/10.13039/501100011033 PID2020-119491GA-I00 (grant PID2020-119491GA-I00) and Generalitat Valenciana (grant CIDEGENT/2020/037). C.M.-V. is the recipient of a predoctoral fellowship from Generalitat Valenciana (CIACIF/2021/329). This work was supported by the Shenzhen Science and Technology Program (Grant No. ZDSYS20230626091659010).Nature Publishing GroupGeneralitat ValencianaGovernment of Guangdong ProvinceAgencia Estatal de InvestigaciónShanxi Scholarship Council of ChinaNational Natural Science Foundation of ChinaDepartment of Education of Guangdong ProvinceRepositorio Institucional de la Universitat Politècnica de València Riunet20252025-05-05journal articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttps://riunet.upv.es/handle/10251/221973reponame:RiuNet. Repositorio Institucional de la Universitat Politécnica de Valénciainstname:Universitat Politècnica de València (UPV)InglésengAgencia Estatal de Investigación http://dx.doi.org/10.13039/501100011033 Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020 PID2020-119491GA-I00 CARACTERIZACION DE UNA RED REGULATORIA DEL RELOJ CIRCADIANO Y SU RECONFIGURACION EN RESPUESTA A DEFICIT DE AGUANational Natural Science Foundation of China https://doi.org/10.13039/501100001809 31670285National Natural Science Foundation of China https://doi.org/10.13039/501100001809 U1904202National Natural Science Foundation of China https://doi.org/10.13039/501100001809 32325031National Natural Science Foundation of China https://doi.org/10.13039/501100001809 32470601National Natural Science Foundation of China https://doi.org/10.13039/501100001809 32300479National Natural Science Foundation of China https://doi.org/10.13039/501100001809 32170259Generalitat Valenciana https://doi.org/10.13039/501100003359 CIDEGENT%2F2020%2F037Generalitat Valenciana https://doi.org/10.13039/501100003359 CIACIF%2F2021%2F329Department of Education of Guangdong Province https://doi.org/10.13039/501100010226 2022KTSCX115Shanxi Scholarship Council of China https://doi.org/10.13039/501100003398 ZDSYS20230626091659010Government of Guangdong Province Government of Guangdong Province 2016ZT06S172Government of Guangdong Province Government of Guangdong Province 2023ZD04073Government of Guangdong Province Government of Guangdong Province 2023A1515011997open accesshttp://purl.org/coar/access_right/c_abf2Reconocimiento - No comercial - Sin obra derivada (by-nc-nd) http://creativecommons.org/licenses/by-nc-nd/4.0/info:eu-repo/semantics/openAccessoai:riunet.upv.es:10251/2219732026-06-13T07:49:27Z
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