Chloroplast perturbations activate retrograde signalling pathways, causing dynamic changes of gene expression. Besides transcriptional control of gene expression, different classes of small non‐coding RNAs (sRNAs) act in gene expression control, but comprehensive analyses regarding their role in retrograde signalling are lacking. We performed sRNA profiling in response to norflurazon (NF), which provokes retrograde signals, in Arabidopsis thaliana wild type (WT) and the two retrograde signalling mutants gun1 and gun5. The RNA samples were also used for mRNA and long non‐coding RNA profiling to link altered sRNA levels to changes in the expression of their cognate target RNAs. We identified 122 sRNAs from all known sRNA classes that were responsive to NF in the WT. Strikingly, 142 and 213 sRNAs were found to be differentially regulated in both mutants, indicating a retrograde control of these sRNAs. Concomitant with the changes in sRNA expression, we detected about 1500 differentially expressed mRNAs in the NF‐treated WT and around 900 and 1400 mRNAs that were differentially regulated in the gun1 and gun5 mutants, with a high proportion (~30%) of genes encoding plastid proteins. Furthermore, around 20% of predicted miRNA targets code for plastid‐localised proteins. Among the sRNA–target pairs, we identified pairs with an anticorrelated expression as well pairs showing other expressional relations, pointing to a role of sRNAs in balancing transcriptional changes upon retrograde signals. Based on the comprehensive changes in sRNA expression, we assume a considerable impact of sRNAs in retrograde‐dependent transcriptional changes to adjust plastidic and nuclear gene expression.

中文翻译：

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鉴定拟南芥中与GUN1和GUN5相关的逆行信号响应的小型非编码RNA。

叶绿体扰动激活逆行信号通路，引起基因表达的动态变化。除了基因表达的转录控制外，不同类别的小型非编码RNA（sRNA）也可用于基因表达控制，但缺乏有关其在逆行信号中作用的全面分析。我们对拟南芥野生型（WT）和两个逆向信号突变体gun1和gun5中引发逆行信号的norflurazon（NF）进行了sRNA分析。。RNA样品还用于mRNA和长时间非编码RNA谱分析，以将改变的sRNA水平与其同源靶RNA表达的变化联系起来。我们从所有已知的sRNA类中鉴定了对WT中的NF响应的122个sRNA。令人惊讶的是，在这两个突变体中发现142和213个sRNA受到差异调节，表明这些sRNA的逆行控制。伴随sRNA表达的变化，我们在经过NF处理的野生动物中检测到约1500个差异表达的mRNA，在gun1和gun5中检测到约900和1400个mRNA差异调节。突变体，其中有很高比例（〜30％）的编码质体蛋白的基因。此外，约20％的预测miRNA靶标编码质体定位蛋白。在sRNA-靶标对中，我们鉴定了具有反相关表达的对以及显示其他表达关系的对，指出了sRNA在逆行信号平衡转录变化中的作用。基于sRNA表达的全面变化，我们假设sRNA在逆行依赖的转录变化中具有相当大的影响，以调节质体和核基因的表达。