Wang Doudou, Zheng Kaifeng, Long Wenfen, Zhao Liang, Li Wanjie, Xue Xiuhua, Han Shengcheng
Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China.
Academy of Plateau Science and Sustainability of the People's Government of Qinghai Province & Beijing Normal University, Qinghai Normal University, Xining 810008, China.
Int J Mol Sci. 2025 Feb 27;26(5):2086. doi: 10.3390/ijms26052086.
Long non-coding RNAs (lncRNAs) are involved in plant biotic and abiotic stress responses, in which Ca also plays a significant role. There is diversity in the regulation of different gene expressions by cytosolic Ca ([Ca]) and nucleosolic Ca ([Ca]). However, no studies have yet explored the interrelationship between lncRNAs and calcium signaling, nor how calcium signaling regulates the expression of lncRNAs. Here, we use transgenic materials and , which simulate [Ca]- and [Ca]-deficient mutants, respectively, and wild type (WT) materials in response to hyperosmolarity (250 mM sorbitol) or salt stresses (125 mM NaCl) at different time points to obtain RNA-seq data, respectively. Then, we proceed with the screening of lncRNAs, adding 688 new lncRNAs to the known Arabidopsis lncRNA database. Subsequently, through the analysis of differentially expressed lncRNA genes, it was found that cytosolic or nucleosolic calcium signals have distinct regulatory effects on differentially expressed lncRNAs (DElncRNAs) and differentially expressed protein-coding genes (DEPCGs) treated with high-concentration NaCl and sorbitol at different times. Furthermore, through weighted correlation network analysis (WGCNA), it is discovered that under hyperosmolarity and salt stresses, lncRNA-associated PCGs are related to the cell wall structure, the plasma membrane component, and osmotic substances through -regulation. In addition, by screening for -regulatory target PCGs of Ca-regulated lncRNAs related to osmotic stress, we obtain a series of lncRNA-PCG pairs related to water transport, cell wall components, and lateral root formation. Therefore, we expand the existing lncRNA database and obtain a series of lncRNAs and PCGs regulated by [Ca] or [Ca] in response to salt and hyperosmolarity stress, providing a new perspective for subsequent research on lncRNAs. We also explore the and -regulated target PCGs of lncRNAs regulated by calcium signaling, providing new insights for further studying salt stress and osmotic stress.
长链非编码RNA（lncRNAs）参与植物的生物和非生物胁迫反应，其中钙也起着重要作用。胞质钙（[Ca]）和核质钙（[Ca]）对不同基因表达的调控存在差异。然而，尚未有研究探讨lncRNAs与钙信号之间的相互关系，也未涉及钙信号如何调控lncRNAs的表达。在此，我们分别使用模拟[Ca]和[Ca]缺乏突变体的转基因材料以及野生型（WT）材料，在不同时间点对高渗（250 mM山梨醇）或盐胁迫（125 mM NaCl）做出反应，以分别获得RNA测序数据。然后，我们进行lncRNAs的筛选，在已知的拟南芥lncRNA数据库中新增了688条lncRNAs。随后，通过对差异表达的lncRNA基因进行分析，发现胞质或核质钙信号对在不同时间用高浓度NaCl和山梨醇处理的差异表达lncRNAs（DElncRNAs）和差异表达的蛋白质编码基因（DEPCGs）具有不同的调控作用。此外，通过加权基因共表达网络分析（WGCNA）发现，在高渗和盐胁迫下，与lncRNA相关的PCGs通过调控与细胞壁结构、质膜成分和渗透物质相关。另外，通过筛选与渗透胁迫相关的钙调控lncRNAs的调控靶标PCGs，我们获得了一系列与水分运输、细胞壁成分和侧根形成相关的lncRNA-PCG对。因此，我们扩展了现有的lncRNA数据库，并获得了一系列受[Ca]或[Ca]调控以响应盐和高渗胁迫的lncRNAs和PCGs，为后续lncRNAs的研究提供了新的视角。我们还探索了钙信号调控的lncRNAs的调控靶标PCGs，为进一步研究盐胁迫和渗透胁迫提供了新的见解。
