Identification of physical interactions between genomic regions by enChIP-Seq

Accumulating evidence suggests critical roles of physical interactions between genomic regions in the regulation of genome functions including gene expression. However, methods to detect physical interactions between genomic regions with confidence have been limited. Here, we showed that detection of physical interactions between genomic regions is feasible by engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) combined with next-generation sequencing (NGS) (enChIP-Seq). In enChIP-Seq, a target genomic region is captured with an engineered DNA-binding molecule such as the CRISPR system consisting of a catalytically inactive form of Cas9 (dCas9) and small guide RNA (sgRNA). Subsequently, the genomic regions physically interacting with the target genomic region in the captured complex are sequenced by NGS. By using enChIP-Seq, we showed that the 5'HS5 locus regulating expression of the beta-globin genes interacts with multiple genomic regions constitutively or inducibly upon erythroid differentiation in a human erythroleukemia cell line, K562. Interestingly, enChIP-Seq did not detect physical interactions of 5'HS5 with regions in the beta-globin locus previously reported to interact with 5'HS5 by using the chromosome conformation capture (3C) assay. These data suggest that enChIP-Seq might be a useful tool to detect physical interactions of genomic regions for elucidation of molecular mechanisms of regulation of genome functions.