Capture Hi-C in (EV and ZFP661-3HA OE) mESCs and E16.5 mouse forebrains

This assay aimed to investigate the regulatory role of ZFP661 in modulating the permeability of CTCF barriers. To achieve this, we generated Capture Hi-C maps on several regions bound by ZFP661 using E16.5 forebrains from wild-type (WT) and Zfp661 knockout (KO) mice, as well as empty vector (EV) control and ZFP661-3HA overexpressing (OE) mESCs. Our findings reveal that ZFP661 modulates the permeability of CTCF barriers, thereby balancing between the interactions that are trapped at the barriers and those passing over them. Overall design: We compared the interactions being trapped at the barriers and those passing over them in WT and Zfp661 KO E16.5 forebrains, as well as EV control and ZFP661-3HA OE mESCs. For the E16.5 forebrain samples, three pairs of littermates were used, while two biological replicates were used for each genotype in mESCs.