Genome-wide (ChIP-seq) identification of target genes regulated by WRKY33 during submergence stress in Arabidopsis

Junlin Zhang,Jianquan Liu,Huanhuan Liu,Zhenxiang Xi,Jiao Fu,Bao Liu,Tao Ma,Yan Song,Yang Chen

doi:10.1186/s12863-021-00972-5

Abstract

BackgroundHypoxia 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.ResultsUsing 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.ConclusionsOur 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”.

Highlights

Hypoxia induced by flooding causes significant losses to crop production almost every year
We further revealed that WRKY33 together with WRKY12 in up-regulating RAP2.2 expression during submergence response, WRKY33 level is increased in RAP2.2overexpressing plants and further experiments confirmed a positive feedback regulation of WRKY33 by RAP2.2 during submergence response in Arabidopsis thaliana [17]
It has been shown that WRKY33 acts as a key factor in submergence response of Arabidopsis thaliana, the downstream regulatory network governed by WRKY33 is still poorly understood

Summary

Introduction

Hypoxia induced by flooding causes significant losses to crop production almost every year. Transgenic plants overexpressing the WRKY33 gene showed enhanced resistance to submergence stress. This transcription factor may regulate a series of target genes in response to submergence. 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. Previous studies have documented that overexpression of the WRKY33 gene enhances the resistance to oxidative stress [15] and promotes pathogen defense [16]. It has been shown that WRKY33 acts as a key factor in submergence response of Arabidopsis thaliana, the downstream regulatory network governed by WRKY33 is still poorly understood. We used ChIP-seq to identify all WRKY33-targeted genes in response to submergence, which will provide a more clearly regulation pathway mediated by WRKY33

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