Chromosome conformation capture (3C) assays are used to map chromatin interactions genome-wide. Chromatin interaction maps provide insights into the spatial organization of chromosomes and the mechanisms by which they fold. Hi-C and Micro-C are widely used 3C protocols that differ in key experimental parameters including cross-linking chemistry and chromatin fragmentation strategy. To understand how the choice of experimental protocol determines the ability to detect and quantify aspects of chromosome folding we have performed a systematic evaluation of 3C experimental parameters. We identified optimal protocol variants for either loop or compartment detection, optimizing fragment size and cross-linking chemistry. We used this knowledge to develop a greatly improved Hi-C protocol (Hi-C 3.0) that can detect both loops and compartments relatively effectively. In addition to providing benchmarked protocols, this work produced ultra-deep chromatin interaction maps using Micro-C, conventional Hi-C and Hi-C 3.0 for key cell lines used by the 4D Nucleome project.

染色体构象捕获 (3C) 测定用于绘制全基因组染色质相互作用。染色质相互作用图提供了对染色体空间组织及其折叠机制的见解。Hi-C 和 Micro-C 是广泛使用的 3C 协议，它们的关键实验参数不同，包括交联化学和染色质碎片策略。为了了解实验方案的选择如何决定检测和量化染色体折叠方面的能力，我们对 3C 实验参数进行了系统评估。我们确定了用于环或隔室检测的最佳协议变体，优化片段大小和交联化学。我们利用这些知识开发了一个大大改进的 Hi-C 协议 (Hi-C 3. 0）可以相对有效地检测循环和隔间。除了提供基准协议外，这项工作还使用 Micro-C、常规 Hi-C 和 Hi-C 3.0 为 4D Nucleome 项目使用的关键细胞系生成了超深染色质相互作用图。