Genome-wide analysis of brassinosteroid responsive small RNAs in Arabidopsis thaliana
Genome-wide analysis of brassinosteroid responsive small RNAs in Arabidopsis thaliana
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DOI：
10.1007/s13258-020-00964-2
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发表时间：
2020-07
期刊：
影响因子：
2.1
通讯作者：
S. Park;Jae H. Choi;Dong-ha Oh;John C. Johnson;M. Dassanayake;D. Jeong;M. Oh
中科院分区：
文献类型：
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作者：
S. Park;Jae H. Choi;Dong-ha Oh;John C. Johnson;M. Dassanayake;D. Jeong;M. Oh
研究背景类黄酮（BRs）是一类在生理和发育过程中具有重要调节作用的植物激素。小RNA（small RNA）包括小干扰RNA（small interfering RNA）和微小RNA（microRNA，miRNA），是在转录和转录后水平调节基因表达的非蛋白质编码RNA。然而，小RNA在BR反应中的作用还没有得到很好的研究。在这项研究中，我们的目的是确定拟南芥BR反应的小RNA簇和miRNA。此外，BR反应的小RNA对他们的成绩单和靶基因的效果进行了examined.MethodsSmall RNA文库构建从控制和epibrassinolide处理的幼苗表达野生型BRI1-Flag蛋白在其天然启动子在thebri1 - 5突变体。对小RNA文库测序后，通过检查拟南芥基因组的100-nt箱中小RNA的表达水平来鉴定差异表达的小RNA簇。为了鉴定BR响应性miRNA，分析了在miRBase中注册的所有注释的成熟miRNA的表达水平。利用先前发表的RNA-seq数据监测BR响应的差异表达的小RNA簇和miRNA靶基因的表达模式。ResultsIn结果，确定了38个BR响应的小RNA簇，包括30个下调和8个上调簇。这些差异表达的小RNA簇来自miRNA位点、转座子、蛋白质编码基因、假基因等。其中，转基因BRI1积累小RNA，这在野生型中没有发现。该转基因中的小RNA被BR上调，而BRI1mRNA被BR下调。通过分析成熟miRNAs的表达模式，我们鉴定了BR抑制的miR398a-5p和BR诱导的miR156g。尽管miR 398a-5p被BR下调，但其预测的靶点对BR没有反应。然而，SPL3，BR诱导的miR156g的目标，下调BRs.ConclusionBR响应的小RNA和miRNAs在这项研究中确定将提供一个洞察小RNA在BR反应在植物中的作用。特别是，我们认为miR156g/SPL3模块可能在BR介导的拟南芥生长发育中发挥作用。
BackgroundBrassinosteroids (BRs) are a class of phytohormones with important roles in regulating physiological and developmental processes. Small RNAs, including small interfering RNAs and microRNAs (miRNAs), are non-protein coding RNAs that regulate gene expression at the transcriptional and post-transcriptional levels. However, the roles of small RNAs in BR response have not been studied well.ObjectiveIn this study, we aimed to identify BR-responsive small RNA clusters and miRNAs in Arabidopsis. In addition, the effect of BR-responsive small RNAs on their transcripts and target genes were examined.MethodsSmall RNA libraries were constructed from control and epibrassinolide-treated seedlings expressing wild-type BRI1-Flag protein under its native promoter in thebri1-5mutant. After sequencing the small RNA libraries, differentially expressed small RNA clusters were identified by examining the expression levels of small RNAs in 100-nt bins of the Arabidopsis genome. To identify the BR-responsive miRNAs, the expression levels of all the annotated mature miRNAs, registered in miRBase, were analyzed. Previously published RNA-seq data were utilized to monitor the BR-responsive expression patterns of differentially expressed small RNA clusters and miRNA target genes.ResultsIn results, 38 BR-responsive small RNA clusters, including 30 down-regulated and eight up-regulated clusters, were identified. These differentially expressed small RNA clusters were from miRNA loci, transposons, protein-coding genes, pseudogenes and others. Of these, a transgene,BRI1, accumulates small RNAs, which are not found in the wild type. Small RNAs in this transgene are up-regulated by BRs whileBRI1mRNA is down-regulated by BRs. By analyzing the expression patterns of mature miRNAs, we have identified BR-repressed miR398a-5p and BR-induced miR156g. Although miR398a-5p is down-regulated by BRs, its predicted targets were not responsive to BRs. However,SPL3, a target of BR-inducible miR156g, is down-regulated by BRs.ConclusionBR-responsive small RNAs and miRNAs identified in this study will provide an insight into the role of small RNAs in BR responses in plants. Especially, we suggest that miR156g/SPL3 module might play a role in BR-mediated growth and development in Arabidopsis.