A single fiber view of the nucleosome organization of eukaryotic chromatin

Nucleosomes arrange into extended arrays, much like beads on a string. They are often phased at genomic landmarks and are thought to be evenly spaced. Here we tested to what extent this stereotypic organization describes the nucleosome landscape in Saccharomyces cerevisiae using a long-read nucleosome-sequencing technique called Fiber-Seq. Fiber-Seq maps the nucleosome pattern on individual chromatin fibers. As such, it is ideally suited to measure the density of nucleosomes per read and quantitate the nucleosome occupancy throughout the genome. We document substantial deviations from the stereotypical nucleosome organization, with unexpectedly long linker DNAs between individual nucleosomes, genomic regions lacking entire nucleosomes, heterogeneous phasing of arrays, truly irregular spacing of arrays and read-to-read variation in nucleosome densities. We exploited the technology to test mechanistic models for the biogenesis of nucleosome arrays. We can rule out transcription elongation playing a decisive role in array formation and detect signatures for a clamping activity of remodelers of the ISWI and CHD1 families after acute nucleosome depletion in vivo. Given that nucleosomes are cis-regulatory elements, the cell-to-cell heterogeneity that Fiber-Seq uncovers provides much needed information to understand chromatin structure and function.核小体（nucleosome）会组装成延伸的阵列，恰似绳上串珠。它们通常会在基因组标志性区域处形成相位排布，且被认为间距均匀。本研究借助名为Fiber-Seq的长读长核小体测序技术，探究了这种典型组织模式在多大程度上适用于酿酒酵母（Saccharomyces cerevisiae）的核小体图谱。Fiber-Seq可对单条染色质纤维上的核小体模式进行绘图定位，正因如此，该技术非常适合用于测量每一次读段中的核小体密度，并定量全基因组范围内的核小体占据率。我们发现，实际核小体组织与典型模式存在显著偏差：核小体间的连接DNA（linker DNA）长度超出预期、存在完全缺失核小体的基因组区域、阵列的相位排布存在异质性、阵列间距真正不规则，且不同读段间的核小体密度存在差异。我们借助该技术，对核小体阵列生物发生的机制模型进行了验证。我们可以排除转录延伸在阵列形成中发挥决定性作用的可能，并在体内急性核小体耗竭后，检测到ISWI与CHD1家族染色质重塑因子的钳合活性特征。鉴于核小体属于顺式调控元件，Fiber-Seq所揭示的细胞间异质性，为我们理解染色质的结构与功能提供了亟需的信息。