Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education. Jiangxi Agricultural University, Nanchang, 330045, China.
College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China.
BMC Genomics. 2018 Jun 15;19(1):460. doi: 10.1186/s12864-018-4807-6.
Long non-coding RNAs (lncRNAs) have been found to play a vital role in several gene regulatory networks involved in the various biological processes in plants related to stress response. However, systematic analyses of lncRNAs expressed in rice Cadmium (Cd) stress are seldom studied. Thus, we presented the characterization and expression of lncRNAs in rice root development at an early stage in response to Cd stress.
The lncRNA deep sequencing revealed differentially expressed lncRNAs among Cd stress and normal condition. In the Cd stress group, 69 lncRNAs were up-regulated and 75 lncRNAs were down-regulated. Furthermore, 386 matched lncRNA-mRNA pairs were detected for 120 differentially expressed lncRNAs and 362 differentially expressed genes in cis, and target gene-related pathway analyses exhibited significant variations in cysteine and methionine metabolism pathway-related genes. For the genes in trans, overall, 28,276 interaction relationships for 144 lncRNAs and differentially expressed protein-coding genes were detected. The pathway analyses found that secondary metabolites, such as phenylpropanoids and phenylalanine, and photosynthesis pathway-related genes were significantly altered by Cd stress. All of these results indicate that lncRNAs may regulate genes of cysteine-rich peptide metabolism in cis, as well as secondary metabolites and photosynthesis in trans, to activate various physiological and biochemical reactions to respond to excessive Cd.
The present study could provide a valuable resource for lncRNA studies in response to Cd treatment in rice. It also expands our knowledge about lncRNA biological function and contributes to the annotation of the rice genome.
长非编码 RNA（lncRNA）已被发现在植物与应激反应相关的各种生物学过程中的几个基因调控网络中发挥重要作用。然而，水稻镉（Cd）胁迫下表达的 lncRNA 的系统分析研究甚少。因此，我们展示了在 Cd 胁迫早期水稻根发育过程中 lncRNA 的特征和表达。
lncRNA 深度测序显示 Cd 胁迫和正常条件下的差异表达 lncRNA。在 Cd 胁迫组中，有 69 个 lncRNA 上调，75 个 lncRNA 下调。此外，在 cis 中检测到 120 个差异表达 lncRNA 和 362 个差异表达基因的 386 个匹配 lncRNA-mRNA 对，而靶基因相关途径分析显示半胱氨酸和蛋氨酸代谢途径相关基因有显著变化。对于 trans 基因，总共检测到 144 个 lncRNA 和差异表达蛋白编码基因之间的 28276 个相互作用关系。途径分析发现，Cd 胁迫显著改变了次级代谢物（如苯丙烷类和苯丙氨酸）和光合作用途径相关基因。所有这些结果表明，lncRNA 可能在 cis 中调节富含半胱氨酸肽代谢的基因，以及在 trans 中调节次级代谢物和光合作用，以激活各种生理和生化反应来应对过量的 Cd。
本研究为水稻对 Cd 处理的 lncRNA 研究提供了有价值的资源，也扩展了我们对 lncRNA 生物学功能的认识，并有助于水稻基因组的注释。
