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

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 methyltransfer-ases affect DNA methylation. Here, we found that the redundant AT...

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Published in植物学报（英文版） Vol. 64; no. 12; pp. 2438 - 2454
Main Authors Ji-Yun Shang, Xue-Wei Cai, Yin-Na Su, Zhao-Chen Zhang, Xin Wang, Nan Zhao, Xin-Jian He
Format Journal Article
LanguageEnglish
Published Tsinghua Institute of Multidisciplinary Biomedical Research,Tsinghua University,Beijing 100084,China 2022
National Institute of Biological Sciences,Beijing 102206,China%National Institute of Biological Sciences,Beijing 102206,China
Subjects
histone methylation
development
DNA methylation
DNA demethylation
NRPE1
ROS1
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Summary: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 methyltransfer-ases affect DNA methylation. Here, we found that the redundant ATX1–5 proteins are not only re-quired for plant development and viability but also for the regulation of DNA methylation. The ex-pression 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 de-methylation pathway mediates DNA demethyla-tion 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 de-methylation genes. Given that the ATX proteins function as catalytic subunits of COMPASS histone methyltransferase complexes, we also demonstrated that the COMPASS complex com-ponents function as a whole to regulate DNA methylation. This study reveals a previously un-characterized mechanism underlying the regu-lation of DNA methylation.
ISSN:1672-9072