J Integr Plant Biol. ›› 2022, Vol. 64 ›› Issue (12): 2438-2454.DOI: 10.1111/jipb.13406

• Research Articles • Previous Articles     Next Articles

Arabidopsis Trithorax histone methyltransferases are redundant in regulating development and DNA methylation

Ji-Yun Shang1, Xue-Wei Cai1, Yin-Na Su1, Zhao-Chen Zhang1, Xin Wang1, Nan Zhao1 and Xin-Jian He1,2 *   

  1. 1 National Institute of Biological Sciences, Beijing 102206, China
    2 Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 100084,  China

    * Correspondence: Xin-Jian He (hexinjian@nibs.ac.cn)
  • Received:2022-08-08 Accepted:2022-11-09 Online:2022-11-10 Published:2022-12-01

Abstract:

Although the Trithorax histone methyltransferases ATX1–5 are known to regulate development and stress responses by catalyzing histone H3K4 methylation in Arabidopsis thaliana, it is unknown whether and how these histone methyltransferases affect DNA methylation. Here, we found that the redundant ATX1–5 proteins are not only required for plant development and viability but also for the regulation of DNA methylation. The expression and H3K4me3 levels of both RNA-directed DNA methylation (RdDM) genes (NRPE1, DCL3, IDN2, and IDP2) and active DNA demethylation genes (ROS1, DML2, and DML3) were downregulated in the atx1/2/4/5 mutant. Consistent with the facts that the active DNA demethylation pathway mediates DNA demethylation mainly at CG and CHG sites, and that the RdDM pathway mediates DNA methylation mainly at CHH sites, whole-genome DNA methylation analyses showed that hyper-CG and CHG DMRs in atx1/2/4/5 significantly overlapped with those in the DNA demethylation pathway mutant ros1 dml2 dml3 (rdd), and that hypo-CHH DMRs in atx1/2/4/5 significantly overlapped with those in the RdDM mutant nrpe1, suggesting that the ATX paralogues function redundantly to regulate DNA methylation by promoting H3K4me3 levels and expression levels of both RdDM genes and active DNA demethylation genes. Given that the ATX proteins function as catalytic subunits of COMPASS histone methyltransferase complexes, we also demonstrated that the COMPASS complex components function as a whole to regulate DNA methylation. This study reveals a previously uncharacterized mechanism underlying the regulation of DNA methylation.

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