Chromosome conformation capture and its variants have allowed chromatin topology to be interrogated at a superior resolution and throughput than by microscopic methods. Among the method derivatives, 4C-seq (circular chromosome conformation capture, coupled to high-throughput sequencing) is a versatile, cost-effective means of assessing all chromatin interactions with a specific genomic region of interest, making it particularly suitable for interrogating chromatin looping events. We present the principles and procedures for designing and implementing successful 4C-seq experiments.
Keywords: Chromatin fixation; Chromatin loops; Circular chromosome conformation capture; Genome topology; High-throughput sequencing; Inverse PCR; Ligation; Restriction digestion.