Key Laboratory for Bio-resources and Eco-environment & State Key Lab of Hydraulics & Mountain River Engineering, College of Life Science, Sichuan University, Chengdu, 610065, China.
BMC Genom Data. 2021 May 24;22(1):16. doi: 10.1186/s12863-021-00972-5.
Hypoxia induced by flooding causes significant losses to crop production almost every year. However, the molecular network of submergence signaling pathway is still poorly understood. According to previous studies, transgenic plants overexpressing the WRKY33 gene showed enhanced resistance to submergence stress. Thus, this transcription factor may regulate a series of target genes in response to submergence. Here, to determine putative downstream targets of WRKY33 at a genome-wide scale in Arabidopsis thaliana, we performed the chromatin immunoprecipitation sequencing (ChIP-seq) using 35S:FLAG-WRKY33 overexpression transgenic lines (WRKY33-OE) after 24 h of submergence treatment.
Using ChIP-seq data, we identified a total of 104 WRKY33-binding genes under submergence stress (WRKY33BGSs). Most WRKY33BGSs are involved in the oxidation-reduction process, programmed cell death in response to reactive oxygen species, lipid biosynthesis process, and other processes related to stress responses. Moreover, the major motif identified in the WRKY33BGSs promoters is a new cis-element, TCTCTC (named here as "TC box"). This cis-element differs from the previously known W box for WRKY33. Further qPCR experiments verified that genes carrying this motif in their promoters could be regulated by WRKY33 upon submergence treatment.
Our study has identified a new putative binding motif of WRKY33 and recovered numerous previously unknown target genes of WRKY33 during submergence stress. The WRKY33 gene positively participates in flooding response probably by transcriptional regulation of the downstream submergence-related target genes via a "TC box".
水淹引起的缺氧几乎每年都会对作物生产造成重大损失。然而，淹水信号通路的分子网络仍知之甚少。根据先前的研究，过表达 WRKY33 基因的转基因植物表现出对淹水胁迫的增强抗性。因此，该转录因子可能会调节一系列应对淹水的靶基因。在这里，为了在拟南芥中在全基因组范围内确定 WRKY33 的假定下游靶标，我们使用 35S:FLAG-WRKY33 过表达转基因系（WRKY33-OE）在淹水处理 24 小时后进行染色质免疫沉淀测序（ChIP-seq）。
使用 ChIP-seq 数据，我们在淹水胁迫下总共鉴定出 104 个 WRKY33 结合基因（WRKY33BGSs）。大多数 WRKY33BGSs 参与氧化还原过程、对活性氧的程序性细胞死亡、脂质生物合成过程以及与应激反应相关的其他过程。此外，在 WRKY33BGSs 启动子中鉴定出的主要基序是一个新的顺式元件，TCTCTC（在此命名为“TC 盒”）。该顺式元件与先前已知的 WRKY33 的 W 盒不同。进一步的 qPCR 实验验证了携带该基序的基因在其启动子中可以在淹水处理时受到 WRKY33 的调控。
我们的研究鉴定了 WRKY33 的一个新的假定结合基序，并在淹水胁迫期间恢复了大量先前未知的 WRKY33 靶基因。WRKY33 基因可能通过“TC 盒”对下游淹水相关靶基因的转录调控，积极参与水淹响应。
