Center for Molecular Medicine, University Medical Center, Utrecht University, Utrecht, the Netherlands.
Delft Bioinformatics Lab, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, the Netherlands.
Nat Genet. 2018 Aug;50(8):1151-1160. doi: 10.1038/s41588-018-0161-5. Epub 2018 Jul 9.
Chromatin folding contributes to the regulation of genomic processes such as gene activity. Existing conformation capture methods characterize genome topology through analysis of pairwise chromatin contacts in populations of cells but cannot discern whether individual interactions occur simultaneously or competitively. Here we present multi-contact 4C (MC-4C), which applies Nanopore sequencing to study multi-way DNA conformations of individual alleles. MC-4C distinguishes cooperative from random and competing interactions and identifies previously missed structures in subpopulations of cells. We show that individual elements of the β-globin superenhancer can aggregate into an enhancer hub that can simultaneously accommodate two genes. Neighboring chromatin domain loops can form rosette-like structures through collision of their CTCF-bound anchors, as seen most prominently in cells lacking the cohesin-unloading factor WAPL. Here, massive collision of CTCF-anchored chromatin loops is believed to reflect 'cohesin traffic jams'. Single-allele topology studies thus help us understand the mechanisms underlying genome folding and functioning.
染色质折叠有助于调节基因组过程，如基因活性。现有的构象捕获方法通过分析细胞群体中两两染色质接触来描述基因组拓扑结构，但无法辨别单个相互作用是同时发生还是竞争发生。在这里，我们提出了多接触 4C（MC-4C），它应用纳米孔测序来研究单个等位基因的多向 DNA 构象。MC-4C 可以区分协同和随机竞争相互作用，并在细胞亚群中识别以前错过的结构。我们表明，β-珠蛋白超级增强子的单个元件可以聚集形成一个增强子枢纽，该枢纽可以同时容纳两个基因。相邻的染色质域环可以通过它们的 CTCF 结合锚点的碰撞形成玫瑰花结样结构，在缺乏着丝粒卸载因子 WAPL 的细胞中最为明显。在这里，大量碰撞的 CTCF 结合的染色质环被认为反映了“着丝粒交通堵塞”。因此，单等位基因拓扑结构研究有助于我们理解基因组折叠和功能的机制。
