Chromosome Conformation Capture (3C) has emerged as a powerful approach for revealing the conformation and features of three-dimensional (3D) genomic organization. Yet attainment of higher resolution in organisms with compact genomes presents a challenge. Here, we describe modifications in the 3C technique that substantially enhance its resolution and sensitivity when applied to the 3D genome of budding yeast. Keys to our approach include use of a 4 bp cutter, Taq I, for cleaving the genome and quantitative PCR for measuring the frequency of ligation. Most importantly, we normalize the percent digestion at each restriction site to account for variation in accessibility of local chromatin structure under a given physiological condition. This strategy has led to the detection of physical interactions between regulatory elements and gene coding regions as well as intricate, stimulus-specific interchromosomal interactions between activated genes. We provide an algorithm that incorporates these and other modifications and allows quantitative determination of chromatin interaction frequencies in yeast under any physiological condition.

中文翻译：

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检测萌芽酵母中新型顺式和反式相互作用的染色体构象捕获

染色体构象捕获 (3C) 已成为揭示三维 (3D) 基因组组织的构象和特征的有力方法。然而，在具有紧凑基因组的生物体中获得更高分辨率是一项挑战。在这里，我们描述了 3C 技术的修改，这些修改在应用于芽殖酵母的 3D 基因组时大大提高了其分辨率和灵敏度。我们方法的关键包括使用 4 bp 切割器 Taq I 来切割基因组和使用定量 PCR 来测量连接频率。最重要的是，我们将每个限制性位点的消化百分比标准化，以解释在给定生理条件下局部染色质结构可及性的变化。这种策略导致检测调控元件和基因编码区之间的物理相互作用以及激活基因之间复杂的、刺激特异性的染色体间相互作用。我们提供了一种算法，该算法结合了这些和其他修改，并允许在任何生理条件下定量测定酵母中的染色质相互作用频率。