Genome doubling affects pre-miRNA expression in plants

Genome doubling, which results in polyploidy, is common in plants and causes genetic and epigenetic alterations. Several researches are in progress to ascertain the effects of polyploidization at the molecular, physiological, and phenotypic level. Although extensive studies are available in synthetic allopolyploids, less is known about the consequences of autopolyploidization. Here, we present a comprehensive analysis of pre-miRNA expression in diploids vs. tetraploids of five different plant species, including the par excellence model Arabidopsis thaliana. Three conserved pre-miRNAs (pre-miR414, pre-miR5538 and pre-miR5141) abounded in all diploids, although their expression was not detected in the tetraploids. Each miRNA target more than one mRNA transcript, many of them belonging to transcription factors (TF) family, DNA repair mechanisms, and related to stress. By contrast, sixteen pre-miRNAs were found in common in all 2x and 4x. Among them, pre-miRNA482, pre-miRNA2916, and pre-miRNA167 significantly changed their expression, being induced or repressed in tetraploids. Based on our results, a microRNA-target regulation network following polyploidization is proposed, which involves DNA repair, ATP-synthesis, terpenoid biosynthesis, and many transcripts responsive to stress. Overall, the results outlined the critical role of microRNAs mediated responses following autopolyploidization in plants.

导致多倍体（polyploidy）形成的基因组加倍现象在植物中十分普遍，且会引发遗传与表观遗传层面的改变。目前已有多项研究致力于从分子、生理及表型层面解析多倍化（polyploidization）所产生的影响。尽管针对人工合成异源多倍体（synthetic allopolyploids）已有大量研究，但对于同源多倍化（autopolyploidization）所带来的后果，学界的认知仍较为有限。本研究对5种不同植物的二倍体（diploids）与四倍体（tetraploids）的前体microRNA（pre-miRNA）表达模式进行了全面分析，其中包括学界公认的经典模式物种拟南芥（Arabidopsis thaliana）。3种保守的pre-miRNA（pre-miR414、pre-miR5538及pre-miR5141）在所有二倍体中均高表达，但在四倍体中未检测到其转录本。每个microRNA（miRNA）可靶向调控多个mRNA转录本，其中多数转录本隶属于转录因子（Transcription Factor, TF）家族、参与DNA修复通路，且与应激响应相关。与之相对，在所有二倍体与四倍体样本中均检测到16种pre-miRNA的共同表达。其中，pre-miRNA482、pre-miRNA2916及pre-miRNA167的表达量发生了显著变化，在四倍体中呈现出上调或下调的表达模式。基于本研究结果，我们提出了多倍化后miRNA-靶基因调控网络模型，该网络涉及DNA修复、ATP合成（ATP synthesis）、萜类生物合成（terpenoid biosynthesis）以及众多应激响应相关的转录本。综上，本研究结果阐明了miRNA介导的响应在植物同源多倍化过程中的关键作用。