VND7诱导新生木质部形成过程中次生细胞壁生物合成的基因调控网络

Haonan Tong, Hao Chen, Cranos M. Williams
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引用次数: 1

摘要

组学数据的积累使我们能够分析参与不同生物过程的多个基因的协调与合作。基因调控网络(grn)用于描述转录因子与参与不同生物过程的下游基因之间的调控关系。次生细胞壁(SCW)的形成参与了植物许多重要的生物过程,如逆境防御、机械强化、水和营养物质的运输等。基于vnd7诱导的新生SCW形成的时间序列数据,采用多种算法构建GRN,然后基于MYB46实验验证的调节数据对每个GRN模型进行评估。从最优GRN模型中,我们不仅确定了8个先前被证明是SCW形成的主要调节因子,而且还发现了6个新的SCW调节因子,包括EGL3, DREB19, TCP14, BZIP61, RGA2和锌指型TF。通过对受这些tf调控的下游基因的进一步硅注释,我们发现了SCW形成与光合作用和干旱响应过程之间的共同转录程序。总的来说,我们的工作为重建和分析GRN提供了一条途径,以确定基因在生物过程中的功能。
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Gene Regulatory Network of Secondary Cell Wall Biosynthesis during VND7 Induced de novo Xylem Formation
Accumulation of -omics data allows us to analyze the coordination and cooperation of multiple genes involved in different biological processes. Gene regulatory networks (GRNs) are used to characterize the regulatory relationships between transcription factors and downstream genes involved in different biological processes. The secondary cell wall (SCW) formation is involved with many important biological processes in plants, such as stress defense, mechanical reinforcement, and the transportation of water and nutrients. We construct GRNs based on the time-series data of VND7-induced de novo SCW formation using multiple algorithms, and then evaluate each GRN model based on the MYB46 experimental validated regulation data. From the optimal GRN model, we not only identify 8 TFs that have been previously demonstrated as the master regulators of SCW formation, but also show 6 novel SCW regulators which include EGL3, DREB19, TCP14, BZIP61, RGA2, and a zinc-finger type TF. From further in silico annotation of the downstream genes that are regulated by these TFs, we find the shared transcriptional program between the SCW formation and the processes of photosynthesis and drought response. Overall, our work suggests a pipeline for reconstructing and analyzing GRN to pinpoint gene functions in biological processes.
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