A microRNA-microRNA crosstalk network inferred from genome-wide single nucleotide polymorphism variants in natural populations of Arabidopsis thaliana.
A microRNA-microRNA crosstalk network inferred from genome-wide single nucleotide polymorphism variants in natural populations of Arabidopsis thaliana.
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DOI：
10.3389/fpls.2022.958520
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发表时间：
2022
影响因子：
5.6
通讯作者：
Meng, Yijun
中科院分区：
文献类型：
--
作者：
Wu, Xiaomei;Wang, Xuewen;Chen, Wei;Liu, Xunyan;Lin, Yibin;Wang, Fengfeng;Liu, Lulu;Meng, Yijun
关键词：
为了适应多变的自然条件，植物已经进化出几种策略来应对不同的环境胁迫。microRNA（miRNA）介导的基因调控就是其中之一。变体，例如，成熟miRNAs或其靶位点内的单核苷酸多态性（single nucleotide polymorphism，SNPs）可导致调控网络的改变和严重的表型改变。在这项研究中，我们提出了一种新的方法来构建一个miRNA-miRNA串扰网络在拟南芥的基础上的概念，两个合作的miRNA共同的目标是在一个强大的压力下，跨生态型遗传在一起。通过对成熟miRNA及其靶位点内的SNP进行全基因组扫描，我们定义了一个“调控命运谱”，以描述与Col-0的参考基因组相比，在1,135个生态型中miRNA靶调控是静态的（保持）还是动态的（获得或丢失）。通过估计它们对共同靶标的调控命运谱的相似性来鉴定合作miRNA对。可靠的合作miRNA对支持坚实的表达相关性，高PPImiRFS评分，和类似的压力反应。静态和动态miRNA靶调控的不同组合解释了协同miRNA对作用于miRNA保守、表达、同源性和应激反应的各种生物学特征。有趣的是，由两种协同miRNA动态共同调节的靶标更可能对应激反应。因此，胁迫相关基因可能在某些生态类型中承担选择压力，其中miRNA调控胁迫基因的重编程。最后，三个案例研究表明，在特定的生态类型中，重新编程miRNA-miRNA串扰与这些生态类型的气候变量和地理位置有关。我们的研究强调了miRNA-miRNA串扰作为自然种群环境适应的遗传基础的潜力。
To adapt to variable natural conditions, plants have evolved several strategies to respond to different environmental stresses. MicroRNA (miRNA)-mediated gene regulation is one of such strategies. Variants, e.g., single nucleotide polymorphisms (SNPs) within the mature miRNAs or their target sites may cause the alteration of regulatory networks and serious phenotype changes. In this study, we proposed a novel approach to construct a miRNA–miRNA crosstalk network in Arabidopsis thaliana based on the notion that two cooperative miRNAs toward common targets are under a strong pressure to be inherited together across ecotypes. By performing a genome-wide scan of the SNPs within the mature miRNAs and their target sites, we defined a “regulation fate profile” to describe a miRNA–target regulation being static (kept) or dynamic (gained or lost) across 1,135 ecotypes compared with the reference genome of Col-0. The cooperative miRNA pairs were identified by estimating the similarity of their regulation fate profiles toward the common targets. The reliability of the cooperative miRNA pairs was supported by solid expressional correlation, high PPImiRFS scores, and similar stress responses. Different combinations of static and dynamic miRNA–target regulations account for the cooperative miRNA pairs acting on various biological characteristics of miRNA conservation, expression, homology, and stress response. Interestingly, the targets that are co-regulated dynamically by both cooperative miRNAs are more likely to be responsive to stress. Hence, stress-related genes probably bear selective pressures in a certain group of ecotypes, in which miRNA regulations on the stress genes reprogram. Finally, three case studies showed that reprogramming miRNA–miRNA crosstalk toward the targets in specific ecotypes was associated with these ecotypes’ climatic variables and geographical locations. Our study highlights the potential of miRNA–miRNA crosstalk as a genetic basis underlying environmental adaptation in natural populations.
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影响因子：
14.9
作者：
Gene Ontology Consortium
通讯作者：
Gene Ontology Consortium
影响因子：
14.9
作者：
Antonov AV;Dietmann S;Wong P;Lutter D;Mewes HW
通讯作者：
Mewes HW
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14.9
作者：
Balaga O;Friedman Y;Linial M
通讯作者：
Linial M
影响因子：
3.7
作者：
Fahlgren N;Howell MD;Kasschau KD;Chapman EJ;Sullivan CM;Cumbie JS;Givan SA;Law TF;Grant SR;Dangl JL;Carrington JC
通讯作者：
Carrington JC
影响因子：
14.9
作者：
Dalmadi, Agnes;Gyula, Peter;Havelda, Zoltan
通讯作者：
Havelda, Zoltan