Chromatin Interaction Maps of Trypanosoma cruzi

Chromatin plays essential roles in all nuclear processes, and the dynamic regulation of its accessibility is critical for orchestrating gene expression programs. Chromosome conformation capture (Hi-C) combines chromosome conformation capture (3C) techniques with next-generation sequencing (NGS) to map physical interactions between distant chromatin regions, enabling genome-wide analysis of three-dimensional genome architecture. We previously conducted the first Hi-C analysis of Trypanosoma cruzi to explore its spatial genome organization and its potential role in gene expression regulation. This chapter describes the experimental procedures for preparing 3C and Hi-C libraries and computational tools for data analysis.