The specificity landscape of WRKY transcription factors reveals the bidirectional influence of non-CG methylation

A distinct epigenetic feature of plants is the DNA methylation in non-CG contexts. Although the physiological roles of non-CG methylation have been elucidated, its direct impact on transcription factor (TF)-DNA interactions remains largely unexplored. Focusing on WRKY-family TFs, here we investigated how non-CG methylation influences their DNA binding specificity and genome-wide cis-regulatory elements (CREs). By generating 461 SELEX and DAP-seq libraries for 54 AtWRKYs, we show that DNA methylation alters both monomeric and dimeric binding specificities of WRKYs, leading to an overall increase in specificity divergence among family members. We curated 201 WRKY motifs and clustered them into 11 classes, 5 of which represent previously unreported specificities. Notably, the known WRKY cis-element PRE4 was found to be recognized only when methylated. The comprehensive dataset of accurate WRKY motifs also enabled the identification of the amino acid discriminants of W-box and WT-box. Expanding on prior knowledge, we demonstrate that methylation not only decreases but can also increase the affinity of WRKYs. This bidirectional effect has globally reshaped the genomic binding landscape of WRKYs upon methylation. Finally, we constructed the WRKY Regulatory Code Database (https://transysbio.cn/WRKYRCDB.php) to facilitate data access.

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Publication Details

Journal
Nucleic Acids Research
Published
2025-11-13
DOI
https://doi.org/10.1093/nar/gkaf1168
Citations
1
Primary Topic
Plant Molecular Biology Research
Type
article
Field-Weighted Citation Impact
1.75
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article

The specificity landscape of WRKY transcription factors reveals the bidirectional influence of non-CG methylation

Yimeng Yin, Qing K. Wang, Minna Taipale, Xinfeng Zhang et al.
1 citations
Nucleic Acids Research
Plant Molecular Biology Research
1.75
article

The specificity landscape of WRKY transcription factors reveals the bidirectional influence of non-CG methylation

Yimeng Yin, Qing K. Wang, Minna Taipale, Xinfeng Zhang, Piaojuan Chen, Fangjie Zhu, Jing Huang, Dong Jiang, Honghong Guo, Juncheng Lin, Nana Ma, Shuyan Chen, Qing Liu, Hao Chen, Tian Li, Lin Luo, Zongkai Mu
article en
1 citations

Abstract

A distinct epigenetic feature of plants is the DNA methylation in non-CG contexts. Although the physiological roles of non-CG methylation have been elucidated, its direct impact on transcription factor (TF)-DNA interactions remains largely unexplored. Focusing on WRKY-family TFs, here we investigated how non-CG methylation influences their DNA binding specificity and genome-wide cis-regulatory elements (CREs). By generating 461 SELEX and DAP-seq libraries for 54 AtWRKYs, we show that DNA methylation alters both monomeric and dimeric binding specificities of WRKYs, leading to an overall increase in specificity divergence among family members. We curated 201 WRKY motifs and clustered them into 11 classes, 5 of which represent previously unreported specificities. Notably, the known WRKY cis-element PRE4 was found to be recognized only when methylated. The comprehensive dataset of accurate WRKY motifs also enabled the identification of the amino acid discriminants of W-box and WT-box. Expanding on prior knowledge, we demonstrate that methylation not only decreases but can also increase the affinity of WRKYs. This bidirectional effect has globally reshaped the genomic binding landscape of WRKYs upon methylation. Finally, we constructed the WRKY Regulatory Code Database (https://transysbio.cn/WRKYRCDB.php) to facilitate data access.

Nucleic Acids ResearchVol. 53(21)
South China Agricultural University (CN), Tongji University (CN), University of Helsinki (FI), University of Cambridge (GB), Wellcome Sanger Institute (GB), Karolinska Institutet (SE), Bridge University (SS), Shanghai Ninth People's Hospital (CN), Wihuri Research Institute (FI), Shanghai Center for Brain Science and Brain-Inspired Technology (CN), Fujian Agriculture and Forestry University (CN), Fuzhou University (CN)
Openalex Percentile: Top 11%
Plant Molecular Biology Research
1.75
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