Histone acetylation readers Bdf1 and Yaf9 guide targeting of SWR1 remodeler to +1 nucleosome

The histone variant H2A.Z marking permissive chromatin is preferentially deposited at promoter-proximal +1 nucleosomes by the multicomponent SWR1 chromatin remodeler. Although SWR1 targeting to nucleosome-depleted regions (NDRs) is directed by its free DNA length sensing module, how the remodeler is guided preferentially to flanking +1 nucleosomes has been enigmatic. Here, we show by live-cell, single-molecule tracking (SMT) that SWR1 subunits Bdf1 and Yaf9 harboring bromo and YEATS acetyl-histone reader domains are required for quantitative chromatin binding via distinct kinetic mechanisms: Bdf1 increases SWR1 association, Yaf9-YEATS reduces disassociation. Notably, SMT and genome-wide ChIP-exo reveals Bdf1 and Yaf9 contributions to SWR1 targeting globally and histone exchange at +1 nucleosomes. Our findings highlight the native biochemistry of histone readers and suggest a broadly applicable, two-stage mechanism wherein acetyl-histone interactions initially constrain 3D diffusion of SWR1 to increase local concentration, followed by stochastic 1D diffusion at NDRs with directional capture by acetylated +1 nucleosomes.组蛋白变体H2A.Z作为开放染色质的标记，可被多组分SWR1染色质重塑复合物优先沉积于启动子近端+1核小体处。尽管SWR1向核小体缺失区域（nucleosome-depleted regions，NDRs）的靶向过程由其游离DNA长度感应模块介导，但该重塑复合物如何被优先引导至侧翼+1核小体的机制此前一直未能阐明。本研究通过活细胞单分子追踪（single-molecule tracking，SMT）实验证实，携带溴结构域与YEATS乙酰组蛋白识别结构域的SWR1亚基Bdf1和Yaf9，可通过不同的动力学机制实现定量染色质结合：Bdf1能够增强SWR1的结合缔合，而Yaf9-YEATS则可降低其解离速率。值得注意的是，单分子追踪与全基因组ChIP-exo实验结果显示，Bdf1和Yaf9对SWR1的全局靶向以及+1核小体处的组蛋白替换均具有调控作用。本研究结果阐明了乙酰组蛋白识别蛋白的天然生化机制，并提出了一种具有广泛适用性的两阶段作用模型：首先通过乙酰组蛋白相互作用限制SWR1的三维扩散，以提升其局部浓度；随后在核小体缺失区域发生随机一维扩散，并被乙酰化+1核小体定向捕获。