Mammalian genomes are folded in a hierarchy of compartments, topologically associating domains (TADs), subTADs, and looping interactions. Currently, there is a great need to evaluate the link between chromatin topology and genome function across many biological conditions and genetic perturbations. Hi-C can generate genome-wide maps of looping interactions but is intractable for high-throughput comparison of loops across multiple conditions due to the enormous number of reads (>6 Billion) required per library. Here, we describe 5C-ID, a new version of Chromosome-Conformation-Capture-Carbon-Copy (5C) with restriction digest and ligation performed in the nucleus (in situ Chromosome-Conformation-Capture (3C)) and ligation-mediated amplification performed with a double alternating primer design. We demonstrate that 5C-ID produces higher-resolution 3D genome folding maps with reduced spatial noise using markedly lower cell numbers than canonical 5C. 5C-ID enables the creation of high-resolution, high-coverage maps of chromatin loops in up to a 30 Megabase subset of the genome at a fraction of the cost of Hi-C.

中文翻译：

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5C-ID：采用原位 3C 和双交替引物设计提高染色体构象捕获碳复制分辨率


哺乳动物基因组以区室、拓扑关联域 (TAD)、亚 TAD 和循环相互作用的层次结构折叠。目前，非常需要评估多种生物条件和遗传扰动下染色质拓扑与基因组功能之间的联系。 Hi-C 可以生成循环相互作用的全基因组图谱，但由于每个文库需要大量读取（> 60 亿），因此难以跨多种条件对循环进行高通量比较。在这里，我们描述了 5C-ID，这是染色体构象捕获碳复制 (5C) 的新版本，在细胞核中进行限制性消化和连接（原位染色体构象捕获 (3C)）以及连接介导的扩增采用双交替引物设计进行。我们证明，5C-ID 使用比规范 5C 明显更少的细胞数量生成更高分辨率的 3D 基因组折叠图，并减少空间噪声。 5C-ID 能够在高达 30 兆碱基的基因组子集中创建高分辨率、高覆盖率的染色质环图，而成本仅为 Hi-C 的一小部分。