Orlando Giulia, Kinnersley Ben, Houlston Richard S
Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom.
Curr Protoc Hum Genet. 2018 Jul;98(1):e63. doi: 10.1002/cphg.63. Epub 2018 Jul 6.
Chromosome conformation capture (3C), coupled with next-generation sequencing (Hi-C), provides a means for deciphering not only the principles underlying genome folding and architecture, but more broadly, the role 3D chromatin structure plays in gene regulation and the replication and repair of DNA. The recently implemented modification, in situ Hi-C, maintains nuclear integrity during digestion and ligation steps, reducing random ligation of Hi-C fragments. Although Hi-C allows for genome-wide characterization of chromatin contacts, it requires high-depth sequencing to discover significant contacts. To address this, Capture Hi-C (CHi-C) enriches standard Hi-C libraries for regions of biological interest, for example by specifically targeting gene promoters, aiding identification of biologically significant chromatin interactions compared to conventional Hi-C, for an equivalent number of sequence reads. Illustrating the application of CHi-C applied to genome-wide analysis of chromatin interactions with promoters, we detail the protocols for in situ Hi-C and CHi-C library generation for sequencing, as well as the bioinformatics tools for data analysis. © 2018 by John Wiley & Sons, Inc.
染色体构象捕获技术（3C）与新一代测序技术（Hi-C）相结合，不仅为破译基因组折叠和结构背后的原理提供了一种手段，更广泛地说，还能揭示三维染色质结构在基因调控以及DNA复制和修复中所起的作用。最近实施的改良技术——原位Hi-C，在消化和连接步骤中保持核完整性，减少了Hi-C片段的随机连接。尽管Hi-C能够对全基因组的染色质接触进行表征，但它需要深度测序才能发现显著的接触。为了解决这个问题，捕获Hi-C（CHi-C）技术针对生物学感兴趣的区域富集标准Hi-C文库，例如通过特异性靶向基因启动子，与传统Hi-C相比，在相同数量的序列读数下，有助于识别生物学上显著的染色质相互作用。为说明CHi-C技术在全基因组分析染色质与启动子相互作用中的应用，我们详细介绍了用于测序的原位Hi-C和CHi-C文库构建方案，以及用于数据分析的生物信息学工具。© 2018约翰威立父子出版公司。
