Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France.
Methods Mol Biol. 2022;2532:15-33. doi: 10.1007/978-1-0716-2497-5_2.
Chromosome conformation capture techniques are a set of methods used to determine 3D genome organization through the capture and identification of physical contacts between pairs of genomic loci. Among them, 4C-seq (circular chromosome conformation capture coupled to high-throughput sequencing) allows for the identification and quantification of the sequences interacting with a preselected locus of interest. 4C-seq has been widely used in the literature, mainly to study chromatin loops between enhancers and promoters or between CTCF binding sites and to identify chromatin domain boundaries. As 3D-contacts may be established in an allele-specific manner, we describe an up-to-date allele-specific 4C-seq protocol, starting from the selection of allele-specific viewpoints to Illumina sequencing. This protocol has mainly been optimized for cultured mammalian cells, but can be adapted for other cell types with relatively minor changes in initial steps.
染色体构象捕获技术是一组通过捕获和识别基因组对之间的物理接触来确定三维基因组结构的方法。其中，4C-seq（环状染色体构象捕获与高通量测序相结合）允许鉴定和定量与预选感兴趣的基因座相互作用的序列。4C-seq 在文献中得到了广泛的应用，主要用于研究增强子和启动子之间或 CTCF 结合位点之间的染色质环，并鉴定染色质域边界。由于三维接触可能以等位基因特异性的方式建立，我们描述了一种最新的等位基因特异性 4C-seq 方案，从等位基因特异性观点的选择开始到 Illumina 测序。该方案主要针对培养的哺乳动物细胞进行了优化，但可以通过在初始步骤中进行相对较小的更改来适应其他细胞类型。
