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 cellu...

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Veröffentlicht in:The New phytologist 2024-11
Hauptverfasser: Xu, Jiwei, Shen, Enhui, Guo, Fu, Wang, Kaiqiang, Hu, Yurong, Shen, Leti, Chen, Hongyu, Li, Xiaohan, Zhu, Qian-Hao, Fan, Longjiang, Chu, Qinjie
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Sprache:eng
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Zusammenfassung: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.
ISSN:0028-646X
1469-8137
1469-8137
DOI:10.1111/nph.20269