High resolution maps of nucleosome position and interactions [II]

Chromatin plays a pivotal role in genome expression, maintenance, and replication. To better understand chromatin organization, we developed a novel proximity-tagging method which assigns unique DNA barcodes to molecules that associate in 3D space. Using this method – termed Proximity Copy Paste (PCP) – we mapped the connectivity of individual nucleosomes in Saccharomyces cerevisiae. We show that chromatin is predominantly organized into regularly spaced nucleosome arrays. The properties of the arrays differs according to transcriptional activity with short delocalized arrays dominating the most highly transcribed genes. Additionally, by mapping long-range, multi-way interactions we provide evidence for the longstanding hypothesis that metaphase chromosomes are compacted by arrayed cohesin hubs. Using single-molecule nuclease footprinting data we define distinct chromatin states within a mixed population to show that noncanonical nucleosomes are a stable feature of chromatin. PCP is a versatile method allowing the connectivity of individual molecules to be mapped at high-resolution染色质（Chromatin）在基因组的表达、维持与复制过程中发挥关键作用。为深入解析染色质的三维组织特性，我们开发了一种全新的邻近标记方法：该方法可对三维空间中相互结合的分子赋予独特的DNA条形码（DNA barcode）。我们借助这种被命名为邻近复制粘贴（Proximity Copy Paste，简称PCP）的方法，对酿酒酵母（Saccharomyces cerevisiae）中单核小体的连接关系进行了图谱绘制。研究结果表明，染色质主要以规则间距排布的核小体阵列形式存在。该阵列的特性随转录活性的差异而改变：高度转录的基因区域主要由短小弥散型核小体阵列占据主导。此外，通过绘制长程多向相互作用图谱，我们为长期存在的假说提供了实验证据——中期染色体是由排列成阵列的黏连蛋白枢纽折叠浓缩而成。我们结合单分子核酸酶足迹实验数据，在混合细胞群体中界定了多种不同的染色质状态，证实非经典核小体是染色质的一类稳定特征。PCP是一种通用性极强的方法，可实现高分辨率下单个分子连接关系的图谱绘制。