Cold stress causes dynamic changes in gene expression that are partially caused by small non-coding RNAs since they regulate protein coding transcripts and act in epigenetic gene silencing pathways. Thus, a detailed analysis of transcriptional changes of small RNAs (sRNAs) belonging to all known sRNA classes such as microRNAs (miRNA) and small interfering RNA (siRNAs) in response to cold contributes to an understanding of cold-related transcriptome changes. We subjected A. thaliana plants to cold acclimation conditions (4 °C) and analyzed the sRNA transcriptomes after 3 h, 6 h and 2 d. We found 93 cold responsive differentially expressed miRNAs and only 14 of these were previously shown to be cold responsive. We performed miRNA target prediction for all differentially expressed miRNAs and a GO analysis revealed the overrepresentation of miRNA-targeted transcripts that code for proteins acting in transcriptional regulation. We also identified a large number of differentially expressed cis- and trans-nat-siRNAs, as well as sRNAs that are derived from long non-coding RNAs. By combining the results of sRNA and mRNA profiling with miRNA target predictions and publicly available information on transcription factors, we reconstructed a cold-specific, miRNA and transcription factor dependent gene regulatory network. We verified the validity of links in the network by testing its ability to predict target gene expression under cold acclimation. In A. thaliana, miRNAs and sRNAs derived from cis- and trans-NAT gene pairs and sRNAs derived from lncRNAs play an important role in regulating gene expression in cold acclimation conditions. This study provides a fundamental database to deepen our knowledge and understanding of regulatory networks in cold acclimation.

中文翻译：

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拟南芥冷驯化过程中小RNA的鉴定。

冷应激会导致基因表达的动态变化，部分由小的非编码RNA引起，因为它们调节蛋白质编码转录本并在表观遗传基因沉默途径中起作用。因此，详细分析属于所有已知sRNA类的小RNA（sRNA）的转录变化，例如微RNA（miRNA）和小干扰RNA（siRNA）对寒冷的反应，有助于理解与寒冷相关的转录组变化。我们将拟南芥植物置于冷驯化条件下（4°C），并在3 h，6 h和2 d后分析了sRNA转录组。我们发现了93种冷应答差异表达的miRNA，其中只有14种先前显示为冷应答。我们对所有差异表达的miRNA进行了miRNA靶标预测，并且GO分析揭示了miRNA靶向的转录本的过量表达，该转录本编码在转录调控中起作用的蛋白质。我们还鉴定了大量差异表达的顺式和反式nat-siRNA，以及衍生自长非编码RNA的sRNA。通过将sRNA和mRNA谱分析的结果与miRNA靶标预测以及转录因子的公开信息结合起来，我们构建了一种冷特异性，miRNA和转录因子依赖性基因调控网络。我们通过测试冷预测条件下其预测目标基因表达的能力来验证网络中链接的有效性。在拟南芥中 源自顺式和反式NAT基因对的miRNA和sRNA以及源自lncRNA的sRNA在调节冷驯化条件下的基因表达中起重要作用。这项研究提供了一个基础数据库，可加深我们对冷驯化中的监管网络的了解和了解。