Ruler elements in chromatin remodelers set nucleosome array spacing and phasing

Arrays of regularly spaced nucleosomes dominate chromatin and are often phased, i.e., aligned at reference sites like active promoters. How distances between nucleosomes and distances between phasing sites and nucleosomes are determined remained unclear, specifically, the role of ATP dependent chromatin remodelers in it. Here, we used a genome-wide reconstitution system to probe how yeast remodelers generate phased nucleosome arrays. We find that remodelers bear a structural element named the ‘ruler’ that sets nucleosome spacing, in the order Chd1 < ISW1a < ISW2 < INO80. Structure-based mutagenesis confirmed the functional significance of the ruler element in INO80. Differences in the ruler elements of different remodelers explain the observed nucleosome array features. More generally, we propose that remodelers use their rulers to regulate the direction of nucleosome sliding in response to nucleosome density and environment, leading to nucleosome positioning relative to other nucleosomes, DNA bound factors or DNA sequence elements.规则间隔排布的核小体（nucleosome）阵列是染色质（chromatin）的核心组成形式，且常呈现相位排列特征，即相较于活性启动子等参考位点实现定向对齐。核小体间的间距，以及相位位点与核小体之间的间距是如何被确定的，这一科学问题迄今尚未阐明，其中ATP依赖型染色质重塑因子（ATP-dependent chromatin remodelers）所发挥的作用尤为不明。本研究利用全基因组重构系统（genome-wide reconstitution system），探究酵母染色质重塑因子如何生成相位排列的核小体阵列。研究发现，染色质重塑因子携带有一种被命名为‘标尺’的结构元件，用于设定核小体间距，其调控能力按Chd1 < ISW1a < ISW2 < INO80的顺序依次递增。基于结构的诱变实验证实了INO80中‘标尺’元件的功能重要性。不同染色质重塑因子的‘标尺’元件之间的差异，可解释观测到的核小体阵列特征。更广泛地说，本研究提出，染色质重塑因子可通过其‘标尺’元件，响应核小体密度与环境信号调控核小体滑动的方向，进而实现核小体相对于其他核小体、DNA结合因子或DNA序列元件的精准定位。