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Comparative characterization of the seven H3K4 methyltransferase in Arabidopsis thaliana

ABSTRACT: Methylation of H3 lysine 4 (H3K4me) marks transcribed elements of the eukaryotic genome, and their distribution alters dynamically through developmental stages and environmental change. These dynamic regulations are likely achieved by the combinatorial work of H3K4me writers, which multi-cellular organisms carry multiple copies of. To better understand the chromatin targeting mechanisms of H3K4 methyltransferase in plants, here we comparatively characterized the seven H3K4 methyltransferases (ATX(R)s) in model plants Arabidopsis. This MS dataset, complemented with the ChIP-seq and AlphaScreen, provides a characterization of ATX(R)s protein. This work clarified, in combination with previous results, ATX1-5 (TRX/TRR-type methyltransferase) localizes on loci with specific sets of chromatin modifications and DNA motifs. Notably, ATXR3, the major H3K4me3 methyltransferase in Arabidopsis, was not associated with COMPASS, which suggests H3K4me3 regulation in plants and animals is divergent. Our work provides a foundation for understanding the regulation of H3K4 methyltransferases in plants.

ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress)

SUBMITTER: Tetsuji Kakutani

PROVIDER: PXD055790 | JPOST Repository | Fri Sep 12 00:00:00 BST 2025

REPOSITORIES: jPOST

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			Action	DRS
	20221206_2022G131_e1.mgf	Mgf
	20221206_2022G131_e1.mzTab	Mztab
	20221206_2022G131_e1.raw	Raw
	20221206_2022G131_e2.mgf	Mgf
	20221206_2022G131_e2.mzTab	Mztab

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Comparative characterization of the seven H3K4 methyltransferases in Arabidopsis thaliana

Project description:Methylation of H3 lysine 4 (H3K4me) marks transcribed elements of eukaryotic genome, and their distribution alters dynamically through developmental stages and environmental change. These dynamic regulations are likely achieved by combinatorial work of H3K4me writers, which multi-cellular organisms carry multiple copies of. To better understand the chromatin targeting mechanisms of H3K4 methyltransferase in plants, here we comparatively characterized the seven H3K4 methyltransferases in model plants Arabidopsis. This work clarified, in combination with previous results, ATX1-5 (TRX/TRR-type methyltransferase) localizes on loci with specific sets of chromatin modifications and DNA motifs. Notably, ATX3 localizes to binding motifs of ASR3 and RAP2.11 transcriptional factors and also directly interacts with those TFs. ATXR7(SET1-type) and ATXR3 (non-canonical H3K4 methyltransferase) seemed co-transcriptional. Interestingly, ATXR3, the major H3K4me3 methyltransferase in Arabidopsis, was not associated with COMPASS, which suggests H3K4me3 regulation in plants and animals is divergent. Our work provides a foundation for understanding the regulation of H3K4 methyltransferases in plants.

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SET DOMAIN GROUP 2 is the major histone H3 lysine-4 tri-methyltransferase in Arabidopsis thaliana

Project description:Post-translational modifications of histones play important roles in modulating chromatin structure and regulating gene expression. We have previously shown that over two thirds of Arabidopsis genes contain histone H3 methylation at lysine-4 (H3K4me), and that tri-methylation of H3K4 (H3K4me3) is preferentially located at actively transcribed genes. In addition, several Arabidopsis mutants with locus-specific loss of H3K4me have been found to display various developmental abnormalities. These findings suggest that H3K4me3 may play important roles in maintaining the normal expression of a large number of genes. However, the major enzyme(s) responsible for H3K4me3 has yet to be identified in plants, making it difficult to address questions regarding the mechanisms and functions of H3K4me3. Here we describe the characterization of SET DOMAIN GROUP 2 (SDG2), a large Arabidopsis protein containing a histone lysine methyltransferase domain. We found that SDG2 homologues are highly conserved in plants, and that the Arabidopsis SDG2 gene is broadly expressed during development. In addition, the loss of SDG2 leads to severe and pleiotropic phenotypes as well as the mis-regulation of a large number of genes. Consistent with our finding that SDG2 is a robust and specific H3K4 methyltransferase in vitro, the loss of SDG2 leads to a drastic decrease in H3K4me3 in vivo. Taken together, these results suggest that SDG2 is the major enzyme responsible for H3K4me3 in Arabidopsis, and that SDG2-dependent H3K4m3 is critical for regulating gene expression and plant development.

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