KDM5C-mediated BRD4 recruitment is essential for active states of enhancers and BET inhibitor sensitivity [ChIP-seq]

A series of Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) experiments were conducted to investigate the effect and mechanism of KDM5C on the recruitment of BRD4 to chromatin, and the effect of this process on histone modification and gene expression. We then performed ChIP-seq for BRD4, KDM5C, H3K27ac, H3K4me3, and H3K4me1 in HeLa and its derivatives cell lines. Overall design: ChIP-seq for BRD4 in CaSki, HeLa parental, sgKDM5C, KDM5C_WT, KDM5C_H514K to investigate the effect of KDM5C on BRD4 peaks intensity. ChIP-seq for KDM5C, BRD4, H3K27ac, H3K4me3, H3K4me1 in HeLa parental and sgKDM5C cell lines to investigate the effect of KDM5C depletion on histone modification. ChIP-seq for H3K4me3 in HeLa parental, shBRD4, sgKDM5C, KDM5C_WT, KDM5C_H514K cell lines to explore the effect of BRD4 and KDM5C on H3K4me3 peak width. ChIP-seq for BRD4 in HeLa cells treated with DMSO, or JQ1, or compound 3b, or in combination to detect the synergistic effect of the two drugs on BRD4 peaks intensity.