National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China.
University of Chinese Academy of Sciences, 100049 Beijing, China.
Proc Natl Acad Sci U S A. 2020 Feb 18;117(7):3543-3550. doi: 10.1073/pnas.1914313117. Epub 2020 Jan 30.
The SWR complex edits the histone composition of nucleosomes at promoters to facilitate transcription by replacing the two nucleosomal H2A-H2B (A-B) dimers with H2A.Z-H2B (Z-B) dimers. Swc5, a subunit of SWR, binds to A-B dimers, but its role in the histone replacement reaction was unclear. In this study, we showed that Swc5 uses a tandem DEF/Y motif within an intrinsically disordered region to engage the A-B dimer. A 2.37-Å X-ray crystal structure of the histone binding domain of Swc5 in complex with an A-B dimer showed that consecutive acidic residues and flanking hydrophobic residues of Swc5 form a cap over the histones, excluding histone-DNA interaction. Mutations in Swc5 DEF/Y inhibited the nucleosome editing function of SWR in vitro. Swc5 DEF/Y interacts with histones in vivo, and the extent of this interaction is dependent on the remodeling ATPase of SWR, supporting a model in which Swc5 acts as a wedge to promote A-B dimer eviction. Given that DEF/Y motifs are found in other evolutionary unrelated chromatin regulators, this work provides the molecular basis for a general strategy used repeatedly during eukaryotic evolution to mobilize histones in various genomic functions.
SWR 复合物通过用 H2A.Z-H2B（Z-B）二聚体替换两个核小体 H2A-H2B（A-B）二聚体来编辑启动子处核小体的组蛋白组成，从而促进转录。SWR 的一个亚基 Swc5 与 A-B 二聚体结合，但它在组蛋白替换反应中的作用尚不清楚。在这项研究中，我们表明 Swc5 使用其无规卷曲区域内的串联 DEF/Y 基序来与 A-B 二聚体结合。Swc5 与 A-B 二聚体结合的组蛋白结合结构域的 2.37-Å X 射线晶体结构表明，Swc5 的连续酸性残基和侧翼疏水性残基在组蛋白上形成一个帽子，从而排除了组蛋白-DNA 的相互作用。Swc5 DEF/Y 中的突变抑制了 SWR 在体外的核小体编辑功能。Swc5 DEF/Y 在体内与组蛋白相互作用，并且这种相互作用的程度依赖于 SWR 的重塑 ATP 酶，这支持了 Swc5 作为楔子促进 A-B 二聚体逐出的模型。鉴于 DEF/Y 基序存在于其他进化上不相关的染色质调节因子中，这项工作为在真核生物进化过程中反复用于各种基因组功能中动员组蛋白的通用策略提供了分子基础。
