Targeted high-resolution chromosome conformation capture at genome-wide scale in mouse erythroid cells. Targeted high-resolution chromosome conformation capture at genome-wide scale in mouse erythroid cells

Chromosome conformation capture (3C) provides an adaptable tool through which to study diverse biological questions. Currently, 3C techniques provide either low-resolution interaction profiles across the entire genome, e.g. HiC, or high-resolution interaction profiles at up to several hundred loci, e.g. NG Capture-C and 4C-seq. Generation of high-resolution, genome-wide interaction profiles can feasibly be achieved through efficiency improvements to current high-resolution methods. To this end we systematically tested and removed areas inefficiency in NG Capture-C to develop a new method Nuclear Capture-C, which provides a 300% increase in informative sequencing content. Using Nuclear Capture-C we target 8,026 erythroid promoters in triplicate, showing that this method can achieve high-resolution genome-wide 3C interaction profiles at scale. Overall design: Nu Capture-C was carried out in triplicate with DpnII for ter119+ mouse erythroid cells from F1 hybrid mice (C57BL/6-cross-CBA/J)

染色体构象捕获（Chromosome conformation capture, 3C）是一款可适配多类生物学问题研究的通用工具。当前，3C技术体系可分为两类：一类可提供全基因组范围的低分辨率相互作用图谱（如HiC），另一类仅能在至多数百个基因座上提供高分辨率相互作用图谱（如NG Capture-C与4C-seq）。通过对现有高分辨率3C技术进行效率优化，即可实现高分辨率全基因组相互作用图谱的构建。为此，我们系统测试并移除了NG Capture-C中的低效区域，开发出全新的Nuclear Capture-C技术，该技术可使有效测序信息含量提升300%。我们利用Nuclear Capture-C技术对8026个红系启动子进行了三次生物学重复实验，结果证实该技术可规模化获取高分辨率全基因组3C相互作用图谱。实验整体设计：以DpnII限制性内切酶处理来自F1杂交小鼠（C57BL/6×CBA/J）的ter119阳性小鼠红系细胞，开展三次重复的Nuclear Capture-C（简称Nu Capture-C）实验。