Figure 2:

Schematic overview of Basic Protocol 1. The nuclei isolated from dual-crosslinked cells are permeabilized, and AluI (a four-base-pair cutter of restriction enzyme) is added to the reaction for in situ digestion. Proximity ligation is performed in situ, with a bridge linker after the A-tailing step. Chromatin immunoprecipitation (ChIP) against a specific protein factor is carried out after sonication of the DNA. The de-crosslinked ChIP DNA is tagmented by Tn5 transponase, and the ChIA-PET library is then amplified by PCR and is ready for sequencing analysis.