Isolation of specific genomic regions retaining molecular interactions is 
essential for comprehensive identification of molecules associated with the 
genomic regions. Recently, we developed the engineered DNA-binding 
molecule-mediated chromatin immunoprecipitation (enChIP) technology for 
purification of specific genomic regions. Here, we developed a retroviral 
expression system for enChIP using CRISPR. We showed that the target genomic 
locus can be purified with high efficiency by using this system. We also showed 
that contamination of potential off-target sites is negligible by using this 
system if the guide RNA (gRNA) for the target site has a sufficiently long 
unique sequence in its seed sequence. enChIP combined with stable isotope 
labeling using amino acids in cell culture (SILAC) analysis identified proteins 
whose association with the interferon (IFN) regulatory factor-1 (IRF-1) promoter 
region increases in response to IFNγ stimulation. The list of the associated 
proteins contained many novel proteins in the context of IFNγ-induced gene 
expression as well as proteins related to histone deacetylase complexes whose 
involvement has been suggested in IFNγ-mediated gene expression. Finally, we 
confirmed IFNγ-induced increased association of the identified proteins with the 
IRF-1 promoter by ChIP. Thus, our results showed that the retroviral enChIP 
system using CRISPR would be useful for biochemical analysis of genome functions 
including transcription and epigenetic regulation.