Chromosome conformation capture (3C) techniques are crucial to understanding tissue-specific regulation of gene expression, but current methods generally require large numbers of cells. This hampers the investigation of chromatin architecture in rare cell populations. We present a new low-input Capture-C approach that can generate high-quality 3C interaction profiles from 10 000–20 000 cells, depending on the resolution used for analysis. We also present a PCR-free, sequencing-free 3C technique based on NanoString technology called C-String. By comparing C-String and Capture-C interaction profiles we show that the latter are not skewed by PCR amplification. Furthermore, we demonstrate that chromatin interactions detected by Capture-C do not depend on the degree of cross-linking by performing experiments with varying formaldehyde concentrations.

中文翻译：

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使用低输入Capture-C可靠地检测少量细胞的染色体相互作用

染色体构象捕获（3C）技术对于理解基因表达的组织特异性调节至关重要，但是当前的方法通常需要大量的细胞。这阻碍了稀有细胞群体中染色质结构的研究。我们提出了一种新的低输入Capture-C方法，该方法可以从10,000至20,000个单元生成高质量的3C交互配置文件，具体取决于用于分析的分辨率。我们还提出了一种基于NanoString技术（称为C-String）的无PCR，无测序的3C技术。通过比较C-String和Capture-C的相互作用曲线，我们表明后者不会因PCR扩增而产生偏斜。此外，我们通过执行不同甲醛浓度的实验证明，Capture-C检测到的染色质相互作用不取决于交联程度。