Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA.
Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edyth Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Mol Cell. 2019 Jan 3;73(1):73-83.e6. doi: 10.1016/j.molcel.2018.10.006. Epub 2018 Nov 8.
DNA methylation and H3K9me are hallmarks of heterochromatin in plants and mammals, and are successfully maintained across generations. The biochemical and structural basis for this maintenance is poorly understood. The maintenance DNA methyltransferase from Zea mays, ZMET2, recognizes dimethylation of H3K9 via a chromodomain (CD) and a bromo adjacent homology (BAH) domain, which flank the catalytic domain. Here, we show that dinucleosomes are the preferred ZMET2 substrate, with DNA methylation preferentially targeted to linker DNA. Electron microscopy shows one ZMET2 molecule bridging two nucleosomes within a dinucleosome. We find that the CD stabilizes binding, whereas the BAH domain enables allosteric activation by the H3K9me mark. ZMET2 further couples recognition of H3K9me to an increase in the specificity for hemimethylated versus unmethylated DNA. We propose a model in which synergistic coupling between recognition of nucleosome spacing, H3K9 methylation, and DNA modification allows ZMET2 to maintain DNA methylation in heterochromatin with high fidelity.
DNA 甲基化和 H3K9me 是植物和哺乳动物异染色质的特征，并且可以成功地在代际间维持。这种维持的生化和结构基础还了解甚少。玉米中的维持 DNA 甲基转移酶 ZMET2 通过一个 chromodomain (CD) 和一个溴相邻同源结构域 (BAH) 识别 H3K9 的二甲基化，这两个结构域位于催化结构域的两侧。在这里，我们表明二联体核小体是 ZMET2 的首选底物，DNA 甲基化优先靶向连接 DNA。电子显微镜显示，一个 ZMET2 分子在二联体核小体中桥接两个核小体。我们发现 CD 稳定了结合，而 BAH 结构域使 H3K9me 标记能够进行别构激活。ZMET2 进一步将 H3K9me 的识别与增加对半甲基化与非甲基化 DNA 的特异性相结合。我们提出了一个模型，其中识别核小体间隔、H3K9 甲基化和 DNA 修饰之间的协同偶联允许 ZMET2 以高保真度维持异染色质中的 DNA 甲基化。
