Genome-wide BRD4, PolII and p65 occupancy as well as chromatin modifications in bone marrow derived macrophages from BRD4 conditional KO mice

We are reporting here genome wide distribution of BRD4 in bone marrow derived macrophages at steady state level and in reponse to LPS stimulation. In both condition, BRD4 distribution was found to be widespread in intragenic as well as intergenic regions with enrichment specifically near TSS. Characteristically BRD4 signal were highly enriched on enhancers of some active genes and hence were classified as BRD4 rich super-enhancers (>12kb long stretches). Super-enhancers are formed, in some instances by redistribution of BRD4 on LPS stimulated genes. BRD4 binding well correlated PolII binding at the chromatin acetylated at H3K27, H3K9 and H4tetraK. Interestingly many LPS induced BRD4 independent genes, despite BRD4 loss in the KO, maintained PolII binding at the chromatin enriched with acetylated lysines at H3K27, H3K9 and H4tetraK. Additionally among some BRD4 independent LPS inducible genes we detected stronger p65 enrichment in the KO. In contrast, P65 binding was not detected in BRD4 dependent genes. These observations provided evidence of plasticity of epigenetic changes in retaining inflammatory reponses in macrophages. Bone marrow derived macrophages were obtained from Brd4Fl/Fl;Ert2-cre and Brd4Fl/Fl mice (WT), Brd4 was deleted from the former by treating bone marrow cells with 4-hydroxytamixfen (KO). For inflammatory stimulus differentiated macrophages were treated with LPS (100ng/ml) for 4 hours.