Zhou Jing, Yang Ling-Yu, Chen Xin, Shi Weng-Guang, Deng Shu-Rong, Luo Zhi-Bin
State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.
Front Plant Sci. 2022 May 12;13:890453. doi: 10.3389/fpls.2022.890453. eCollection 2022.
Nitrate (NO ) and ammonium (NH ) are the primary forms of inorganic nitrogen acquired by plant roots. LncRNAs, as key regulators of gene expression, are a class of non-coding RNAs larger than 200 bp. However, knowledge about the regulatory role of lncRNAs in response to different nitrogen forms remains limited, particularly in woody plants. Here, we performed strand-specific RNA-sequencing of roots under three different nitrogen fertilization treatments. In total, 324 lncRNAs and 6,112 mRNAs were identified as showing significantly differential expression between the NO and NHNO treatments. Moreover, 333 lncRNAs and 6,007 mRNAs showed significantly differential expression between the NH and NHNO treatments. Further analysis suggested that these lncRNAs and mRNAs have different response mechanisms for different nitrogen forms. In addition, functional annotation of and target mRNAs of differentially expressed lncRNAs indicated that 60 lncRNAs corresponding to 49 differentially expressed and target mRNAs were involved in plant nitrogen metabolism and amino acid biosynthesis and metabolism. Furthermore, 42 lncRNAs were identified as putative precursors of 63 miRNAs, and 28 differentially expressed lncRNAs were potential endogenous target mimics targeted by 96 miRNAs. Moreover, ceRNA regulation networks were constructed. MSTRG.6097.1, MSTRG.13550.1, MSTRG.2693.1, and MSTRG.12899.1, as hub lncRNAs in the ceRNA networks, are potential candidate lncRNAs for studying the regulatory mechanism in poplar roots under different nitrogen fertilization treatments. The results provide a basis for obtaining insight into the molecular mechanisms of lncRNA responses to different nitrogen forms in woody plants.
硝酸盐（NO ）和铵盐（NH ）是植物根系获取无机氮的主要形式。长链非编码RNA（lncRNAs）作为基因表达的关键调节因子，是一类长度大于200bp的非编码RNA。然而，关于lncRNAs在响应不同氮形态时的调节作用的知识仍然有限，尤其是在木本植物中。在这里，我们对三种不同氮肥处理下的根系进行了链特异性RNA测序。总共鉴定出324个lncRNAs和6112个mRNA在NO 和NHNO处理之间表现出显著差异表达。此外，333个lncRNAs和6007个mRNA在NH 和NHNO处理之间表现出显著差异表达。进一步分析表明，这些lncRNAs和mRNAs对不同氮形态具有不同的响应机制。此外，对差异表达lncRNAs的 和 靶mRNA的功能注释表明，与49个差异表达的 和 靶mRNA对应的60个lncRNAs参与了植物氮代谢以及氨基酸的生物合成和代谢。此外，42个lncRNAs被鉴定为63个miRNA的假定前体，28个差异表达的lncRNAs是96个miRNA靶向的潜在内源性靶标模拟物。此外，构建了ceRNA调控网络。MSTRG.6097.1、MSTRG.13550.1、MSTRG.2693.1和MSTRG.12899.1作为ceRNA网络中的枢纽lncRNAs，是研究不同氮肥处理下杨树根系调控机制的潜在候选lncRNAs。这些结果为深入了解木本植物中lncRNA对不同氮形态的响应分子机制提供了依据。
