Kovrizhnykh V V, Mustafin Z S, Bagautdinova Z Z
Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia.
Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.
Vavilovskii Zhurnal Genet Selektsii. 2021 Feb;25(1):39-45. doi: 10.18699/VJ21.005.
Active polar transport of the plant hormone auxin carried out by its PIN transporters is a key link in the formation and maintenance of auxin distribution, which, in turn, determines plant morphogenesis. The plasticity of auxin distribution is largely realized through the molecular genetic regulation of the expression of its transporters belonging to the PIN-FORMED (PIN) protein family. Regulation of auxin-response genes occurs through the ARF-Aux/ IAA signaling pathway. However, it is not known which ARF-Aux/IAA proteins are involved in the regulation of PIN gene expression by auxin. In Arabidopsis thaliana, the PIN, ARF, and Aux/IAA families contain a larger number of members; their various combinations are possible in realization of the signaling pathway, and this is a challenge for understanding the mechanisms of this process. The use of high-throughput sequencing data on auxin-induced transcriptomes makes it possible to identify candidate genes involved in the regulation of PIN expression. To address this problem, we created an approach for the meta-analysis of auxin-induced transcriptomes, which helped us select genes that change their expression during the auxin response together with PIN1, PIN3, PIN4 and PIN7. Possible regulators of ARF-Aux/ IAA signaling pathway for each of the PINs under study were identif ied, and so were the aspects of their regulatory circuits both common for groups of PIN genes and specif ic for each PIN gene. Reconstruction of gene networks and their analysis predicted possible interactions between genes and served as an additional conf irmation of the pathways obtained in the meta-analysis. The approach developed can be used in the search for gene expression regulators in other genomewide data.
植物激素生长素通过其PIN转运蛋白进行的主动极性运输是生长素分布形成和维持的关键环节，而生长素分布又决定了植物的形态发生。生长素分布的可塑性很大程度上是通过对其属于PIN-FORMED（PIN）蛋白家族的转运蛋白表达的分子遗传调控来实现的。生长素应答基因的调控通过ARF-Aux/IAA信号通路进行。然而，尚不清楚哪些ARF-Aux/IAA蛋白参与生长素对PIN基因表达的调控。在拟南芥中，PIN、ARF和Aux/IAA家族包含大量成员；它们在信号通路的实现中可能有多种组合，这对理解该过程的机制构成了挑战。利用生长素诱导转录组的高通量测序数据能够鉴定参与PIN表达调控的候选基因。为了解决这个问题，我们创建了一种对生长素诱导转录组进行荟萃分析的方法，这有助于我们筛选出在生长素应答过程中与PIN1、PIN3、PIN4和PIN7一起改变表达的基因。确定了每个研究的PIN的ARF-Aux/IAA信号通路的可能调节因子，以及它们的调控回路中PIN基因组共有的方面和每个PIN基因特有的方面。基因网络的重建及其分析预测了基因之间可能的相互作用，并作为对荟萃分析中获得的通路的额外证实。所开发的方法可用于在其他全基因组数据中寻找基因表达调节因子。
