从单细胞转录组中鉴定植物长链核糖核酸的细胞类型特异性、反式和顺式作用功能。

IF 8.3 1区生物学 Q1 PLANT SCIENCES

New Phytologist Pub Date : 2024-11-17 DOI:10.1111/nph.20269

Jiwei Xu, Enhui Shen, Fu Guo, Kaiqiang Wang, Yurong Hu, Leti Shen, Hongyu Chen, Xiaohan Li, Qian-Hao Zhu, Longjiang Fan, Qinjie Chu

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引用次数: 0

摘要

长非编码 RNA，包括基因间 lncRNA（lincRNA），在植物整个生命周期的各种生物过程中发挥着关键作用，单细胞 RNA 测序（scRNA-seq）技术的出现为研究 lincRNA 在细胞过程中的复杂作用开辟了一条宝贵的途径。在这里，我们利用来自不同植物组织（水稻、拟南芥、番茄和玉米）的 scRNA-seq 数据鉴定了一批新的 lincRNAs。基于完善注释的单细胞转录组图谱，我们发现植物 lincRNAs 与 mRNAs 具有相同程度的细胞类型特异性，并根据伪时间分析参与了某些细胞类型的分化。许多 lincRNAs 被预测在细胞类型特异性 lincRNAs 和 mRNAs 的共表达网络中发挥枢纽作用，这表明它们具有反式作用能力。此外，根据其基因组距离以及与邻近mRNA的表达相关性，发现植物lincRNA具有潜在的顺式作用特性。此外，我们还构建了一个在线平台 PscLncRNA (http://ibi.zju.edu.cn/psclncrna/)，用于搜索和可视化所有已发现的具有潜在功能注释的植物 lincRNAs。我们的工作为单细胞分辨率下的植物 lincRNAs 提供了新的见解，也为了解和进一步研究植物 lincRNAs 提供了重要资源。

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Identification of cell-type specificity, trans- and cis-acting functions of plant lincRNAs from single-cell transcriptomes

Long noncoding RNAs, including intergenic lncRNAs (lincRNAs), play a key role in various biological processes throughout the plant life cycle, and the advent of single-cell RNA sequencing (scRNA-seq) technology has opened up a valuable avenue for scrutinizing the intricate roles of lincRNAs in cellular processes.
Here, we identified a new batch of lincRNAs using scRNA-seq data from diverse tissues of plants (rice, Arabidopsis, tomato, and maize). Based on well-annotated single-cell transcriptome atlases, plant lincRNAs were found to possess the same level of cell-type specificity as mRNAs and to be involved in the differentiation of certain cell types based on pseudo-time analysis.
Many lincRNAs were predicted to play a hub role in the cell-type-specific co-expression networks of lincRNAs and mRNAs, suggesting their trans-acting abilities. Besides, plant lincRNAs were revealed to have potential cis-acting properties based on their genomic distances and expression correlations with the neighboring mRNAs.
Furthermore, an online platform, PscLncRNA (http://ibi.zju.edu.cn/psclncrna/), was constructed for searching and visualizing all identified plant lincRNAs with annotated potential functions. Our work provides new insights into plant lincRNAs at single-cell resolution and an important resource for understanding and further investigation of plant lincRNAs.

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来源期刊

New Phytologist 生物-植物科学

自引率

5.30%

发文量

728

期刊介绍： New Phytologist is an international electronic journal published 24 times a year. It is owned by the New Phytologist Foundation, a non-profit-making charitable organization dedicated to promoting plant science. The journal publishes excellent, novel, rigorous, and timely research and scholarship in plant science and its applications. The articles cover topics in five sections: Physiology & Development, Environment, Interaction, Evolution, and Transformative Plant Biotechnology. These sections encompass intracellular processes, global environmental change, and encourage cross-disciplinary approaches. The journal recognizes the use of techniques from molecular and cell biology, functional genomics, modeling, and system-based approaches in plant science. Abstracting and Indexing Information for New Phytologist includes Academic Search, AgBiotech News & Information, Agroforestry Abstracts, Biochemistry & Biophysics Citation Index, Botanical Pesticides, CAB Abstracts®, Environment Index, Global Health, and Plant Breeding Abstracts, and others.