Ganie Showkat Ahmad, Dey Narottam, Mondal Tapan Kumar
Division of Genomic Resources, National Bureau of Plant Genetic Resources, IARI Campus, New Delhi, 110012, India.
Department of Biotechnology, Visva-Bharati, Santiniketan, 731 235, West Bengal, India.
Funct Integr Genomics. 2016 Jan;16(1):1-11. doi: 10.1007/s10142-015-0460-1. Epub 2015 Aug 29.
MicroRNAs (miRNAs) are important molecules that regulate gene expression under salinity stress. Despite their evolutionary conservation, these regulatory elements have been shown to behave differently in different plant species under a particular environmental stress. In this study, we investigated the behavior of salt responsive osa-miR393a and its target gene (TIR1, LOC_Os05g05800) in salt-tolerant (FL478) and salt-sensitive (IR29) rice genotypes. It was found that the mature and precursor sequences of osa-miR393a as well as its cleavage site in TIR1 were conserved among salt tolerant and sensitive genotypes. Promoters of different salt-responsive miRNAs were also found to be less variable between salt-tolerant and salt-susceptible genotypes. Analysis of gene expression, promoter methylation, and cis-element abundance showed that osa-miR393a behaves differently in FL478 and IR29. Salt stress altered the expression pattern of osa-miR393a-TIR1 module in a time-dependent manner in the roots and shoots of two genotypes. Promoter methylation of this regulatory module was also altered at different time points under salt stress. Expression analysis in two genotypes indicated the overall down-regulation of osa-miR393a and up-regulation of TIR1 in FL478 and their reciprocal regulation in IR29. The expression results were complemented by the differential promoter methylation and cis-element abundance of this regulatory module. Together, the results of transcript abundance and promoter methylation of osa-miR393a-TIR1 module signified the association between these two processes which is reported for the first time in plants to the best of our knowledge.
微小RNA（miRNA）是在盐胁迫下调节基因表达的重要分子。尽管它们具有进化保守性，但这些调控元件在特定环境胁迫下在不同植物物种中的表现有所不同。在本研究中，我们调查了耐盐（FL478）和盐敏感（IR29）水稻基因型中盐响应性osa-miR393a及其靶基因（TIR1，LOC_Os05g05800）的行为。结果发现，osa-miR393a的成熟序列、前体序列及其在TIR1中的切割位点在耐盐和敏感基因型中是保守的。不同盐响应性miRNA的启动子在耐盐和盐敏感基因型之间也显示出较小的变异性。基因表达、启动子甲基化和顺式元件丰度分析表明，osa-miR393a在FL478和IR29中的行为不同。盐胁迫以时间依赖的方式改变了两种基因型根和茎中osa-miR393a-TIR1模块的表达模式。该调控模块的启动子甲基化在盐胁迫下的不同时间点也发生了改变。两种基因型中的表达分析表明，osa-miR393a在FL478中总体下调，TIR1上调，而在IR29中则相反。表达结果得到了该调控模块启动子甲基化差异和顺式元件丰度的补充。总之，osa-miR393a-TIR1模块的转录本丰度和启动子甲基化结果表明了这两个过程之间的关联，据我们所知，这在植物中是首次报道。
