ChIA-PET Analysis for Investigating SMC-Mediated 3D Genomic Contacts

We present a detailed ChIA-PET benchwork protocol optimized for investigating cohesin- and condensin-mediated chromatin contacts. This method combines chromatin immunoprecipitation (ChIP), proximity ligation, EcoP15I digestion, and sequencing library construction to achieve high specificity in detecting SMC-dependent genomic contacts. Key quality control measures, including ChIP DNA validation, linker ligation strategies, and PCR cycle optimization, are outlined to enhance data reliability. By providing a genome-wide view of SMC-driven chromatin contacts, this method offers valuable insights into the fundamental principles of genome folding and maintenance.