High-Throughput Chromosome Conformation Capture Immunoprecipitation in Skeletal Muscle Stem Cells

Fate determination of muscle stem cells (MuSCs) is associated with the regulation of gene expression across multiple layers of chromatin organization, ranging from local chromatin accessibility to higher-order three-dimensional (3D) genome architecture driven by transcription factors, architectural proteins, and histone marks. Advancements in chromosome conformation capture (3C) technologies have facilitated the mapping of regulatory interactions with increasing precision. HiChIP-based genome-wide detection of chromatin interactions mediated by chromatin-bound proteins or histone modifications provides an optimal genomic reference for high-resolution detection of changes in 3D genome architecture. However, analyzing the regulation of chromatin conformation defined by specific proteins and integrating it robustly with chromatin accessibility and gene expression remains technically challenging in MuSCs. In this chapter, we present a reproducible workflow to generate a HiChIP dataset from a limited number of MuSCs. Finally, we provide integration tools/workflow to integrate HiChIP datasets with ATAC-seq and RNA-seq datasets.