Mapping the 3D Chromosome Organization of a Biosynthetic Gene Cluster by Capture Hi-C (CHi-C)

Chromosome conformation capture (3C), when combined with high-throughput next-generation sequencing, known as Hi-C, is a powerful approach for visualizing three-dimensional genome architecture. This technique enables detailed study of how chromosome topology influences gene regulation and other key cellular processes.Incorporating a sequence capture step into the Hi-C workflow enables targeted enrichment of predefined genomic regions of interest. Compared with conventional Hi-C, Capture Hi-C (CHi-C) increases the sequencing depth for the targeted regions, enabling high-resolution analysis of chromatin structure within a predefined locus at a lower cost.Here, we present a detailed protocol for CHi-C applied to a region of the Arabidopsis thaliana genome encompassing the thalianol biosynthetic gene cluster.