Disclosed is a method for isolating a genome region specifically while maintaining an interaction state between the genome region and a molecule that has been interacted with the genome region. A specific genome region can be isolated while maintaining an interaction state between the genome region and a molecule that has been interacted with the genome region by employing a process comprising the steps (1) to (5) mentioned below: (1) preparing cells in each of which a DNA fragment containing a recognition sequence for a foreign DNA binding molecule is inserted into genomic DNA of the genome region to be isolated; (2) bringing a foreign molecule containing at least a DNA binding domain of the foreign DNA binding molecule into contact with the genomic DNA of each of the cells; (3) carrying out a treatment for maintaining an interaction state between the genomic DNA of each of the cells and a molecule that has been interacted with the genomic DNA; (4) carrying out a treatment for fragmenting the genomic DNA; and (5) binding a molecule capable of specifically binding to the foreign molecule to produce a complex and collecting the complex.
