Capture Hi-C Library Generation and Analysis to Detect Chromatin Interactions

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.