An Arabidopsis single-nucleus atlas decodes leaf senescence and nutrient allocation

IF 45.5 1区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY

Cell Pub Date : 2025-04-11 DOI:10.1016/j.cell.2025.03.024

Xing Guo, Yichuan Wang, Caiyao Zhao, Cong Tan, Wei Yan, Sunhuan Xiang, Dan Zhang, Hui Zhang, Mengting Zhang, Liujing Yang, Meng Yan, Pingli Xie, Yi Wang, Li Li, Dongming Fang, Xuanmin Guang, Wenwen Shao, Fang Wang, Haoxuan Wang, Sunil Kumar Sahu, Xun Xu

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引用次数: 0

Abstract

With rapid advancements in single-cell RNA sequencing (scRNA-seq) technologies, exploration of the systemic coordination of critical physiological processes has entered a new era. Here, we generated a comprehensive Arabidopsis single-nucleus transcriptomic atlas using over 1 million nuclei from 20 tissues encompassing multiple developmental stages. Our analyses identified cell types that have not been characterized in previous single-protoplast studies and revealed cell-type conservation and specificity across different organs. Through time-resolved sampling, we revealed highly coordinated onset and progression of senescence among the major leaf cell types. We originally formulated two molecular indexes to quantify the aging state of leaf cells at single-cell resolution. Additionally, facilitated by weighted gene co-expression network analysis, we identified hundreds of promising hub genes that may integratively regulate leaf senescence. Inspired by the functional validation of identified hub genes, we built a systemic scenario of carbon and nitrogen allocation among different cell types from source leaves to sink organs.

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随着单细胞 RNA 测序（scRNA-seq）技术的快速发展，对关键生理过程的系统协调的探索进入了一个新时代。在这里，我们利用来自 20 个组织、涵盖多个发育阶段的 100 多万个细胞核，生成了一个全面的拟南芥单核转录组图谱。我们的分析确定了以前的单原核研究中没有表征的细胞类型，并揭示了不同器官中细胞类型的保守性和特异性。通过时间分辨取样，我们揭示了主要叶细胞类型之间高度协调的衰老开始和进展。我们最初制定了两个分子指标，以单细胞分辨率量化叶细胞的衰老状态。此外，在加权基因共表达网络分析的帮助下，我们发现了数百个可能综合调控叶片衰老的中枢基因。在对所发现的中心基因进行功能验证的启发下，我们构建了一个从源叶到汇器官的不同细胞类型之间碳和氮分配的系统情景。

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来源期刊

Cell 生物-生化与分子生物学

CiteScore

110.00

自引率

0.80%

发文量

396

审稿时长

2 months

期刊介绍： Cells is an international, peer-reviewed, open access journal that focuses on cell biology, molecular biology, and biophysics. It is affiliated with several societies, including the Spanish Society for Biochemistry and Molecular Biology (SEBBM), Nordic Autophagy Society (NAS), Spanish Society of Hematology and Hemotherapy (SEHH), and Society for Regenerative Medicine (Russian Federation) (RPO). The journal publishes research findings of significant importance in various areas of experimental biology, such as cell biology, molecular biology, neuroscience, immunology, virology, microbiology, cancer, human genetics, systems biology, signaling, and disease mechanisms and therapeutics. The primary criterion for considering papers is whether the results contribute to significant conceptual advances or raise thought-provoking questions and hypotheses related to interesting and important biological inquiries. In addition to primary research articles presented in four formats, Cells also features review and opinion articles in its "leading edge" section, discussing recent research advancements and topics of interest to its wide readership.