Mapping the 3D Chromosome Organization of Streptomyces by Hi-C

Streptomyces species are prolific producers of bioactive compounds, including antibiotics, but many of their biosynthetic gene clusters (BGCs) remain silent or are poorly expressed under laboratory conditions. Recent studies have reported a close correlation between chromosomal organization and the expression activity of genes, including BGCs. Chromosome conformation capture with high-throughput sequencing (Hi-C) is a technique that allows for the profiling of three-dimensional genome organization by capturing physical interactions between chromosomal regions. In this chapter, we describe the application of Hi-C to Streptomyces coelicolor, focusing on the detailed protocol for constructing a Hi-C library and analyzing chromosomal interactions. By using this technique, researchers can explore the relationship between chromosomal architecture and the expression of BGCs, which may inform new strategies for improving natural product yields in Streptomyces.