AtHDA6 functions as an H3K18ac eraser to maintain pericentromeric CHG 
methylation in Arabidopsis thaliana

Wang, Qianwen; Bao, Xiucong; Chen, Shengjie; Zhong, Huan; Liu, Yaqin; Zhang, Li; Xia, Yiji; Kragler, F.; Luo, Ming; Li, Xiang David; Lam, Hon-Ming; Zhang, Shoudong

doi:10.1093/nar/gkab706

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AtHDA6 functions as an H3K18ac eraser to maintain pericentromeric CHG methylation in Arabidopsis thaliana

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Kragler, F.
Intercellular Macromolecular Transport, Department Stitt, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

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Citation

Wang, Q., Bao, X., Chen, S., Zhong, H., Liu, Y., Zhang, L., et al. (2021). AtHDA6 functions as an H3K18ac eraser to maintain pericentromeric CHG methylation in Arabidopsis thaliana. Nucleic Acids Research, 49(17), 9755-9767. doi:10.1093/nar/gkab706.

Cite as: https://hdl.handle.net/21.11116/0000-0009-0DA3-1

Abstract

Pericentromeric DNA, consisting of high-copy-number tandem repeats and transposable elements, is normally silenced through DNA methylation and histone modifications to maintain chromosomal integrity and stability. Although histone deacetylase 6 (HDA6) has been known to participate in pericentromeric silencing, the mechanism is still yet unclear. Here, using whole genome bisulfite sequencing (WGBS) and chromatin immunoprecipitation-sequencing (ChIP-Seq), we mapped the genome-wide patterns of differential DNA methylation and histone H3 lysine 18 acetylation (H3K18ac) in wild-type and hda6 mutant strains. Results show pericentromeric CHG hypomethylation in hda6 mutants was mediated by DNA demethylases, not by DNA methyltransferases as previously thought. DNA demethylases can recognize H3K18ac mark and then be recruited to the chromatin. Using biochemical assays, we found that HDA6 could function as an ‘eraser’ enzyme for H3K18ac mark to prevent DNA demethylation. Oxford Nanopore Technology Direct RNA Sequencing (ONT DRS) also revealed that hda6 mutants with H3K18ac accumulation and CHG hypomethylation were shown to have transcriptionally active pericentromeric DNA.