School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region.
Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region.
Nucleic Acids Res. 2021 Sep 27;49(17):9755-9767. doi: 10.1093/nar/gkab706.
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.
着丝粒周围 DNA 由高拷贝数串联重复序列和转座元件组成，通常通过 DNA 甲基化和组蛋白修饰沉默，以维持染色体的完整性和稳定性。尽管组蛋白去乙酰化酶 6（HDA6）已被证明参与着丝粒沉默，但机制仍不清楚。在这里，我们使用全基因组亚硫酸氢盐测序（WGBS）和染色质免疫沉淀测序（ChIP-Seq），绘制了野生型和 hda6 突变菌株中全基因组差异 DNA 甲基化和组蛋白 H3 赖氨酸 18 乙酰化（H3K18ac）的图谱。结果表明，hda6 突变体中着丝粒周围的 CHG 低甲基化是由 DNA 去甲基化酶介导的，而不是像以前认为的那样由 DNA 甲基转移酶介导。DNA 去甲基化酶可以识别 H3K18ac 标记，然后被招募到染色质上。通过生化分析，我们发现 HDA6 可以作为 H3K18ac 标记的“橡皮擦”酶，防止 DNA 去甲基化。牛津纳米孔技术直接 RNA 测序（ONT DRS）还表明，H3K18ac 积累和 CHG 低甲基化的 hda6 突变体显示出转录活性的着丝粒周围 DNA。
