Bromodomain inhibition of the co-activators CBP/EP300 facilitates reprogramming (ChIP-seq II)

Silencing of the somatic cell-type specific gene expression programs is a critical yet poorly understood step in nuclear reprogramming. To uncover chromatin-related pathways important for maintaining cell identity, we carried out a reprogramming screen using inhibitors of chromatin factors. Here we identify two independent acetyl-lysine competitive inhibitors targeting the bromodomains of coactivators EP300 and CBP as potent enhancers of reprogramming. EP300/CBP bromodomain inhibition is critical during early stages of reprogramming, significantly accelerates the emergence of iPSCs and, when combined with Dot1L inhibition, enables efficient derivation of human iPSCs with Oct4 and Sox2 alone. In contrast, complete inhibition of catalytic acetyl-transferase activity of EP300/CBP prevents reprogramming. Genome-wide expression analyses indicate that EP300/CBP bromodomain inhibition diminishes the expression of somatic-specific genes without affecting the induction of pluripotency regulators. Through expression analyses, we identify the master mesenchymal transcription factor PRRX1 as a functionally important target in reprogramming that is downregulated upon EP300/CBP bromodomain inhibition. Collectively, our data uncover a role for bromodomain-mediated interactions of EP300/CBP in sustaining cell type specific gene expression programs and maintaining somatic cell identity Overall design: Examination of H3K27ac, H3K18ac, H3K4me1 and H3K4me3 histone modifications in iPSC cells. Antibodies used: H3K27ac: Active Motif 39133 H3K18ac: Abcam ab1191 H3K4me1: Diagenode C15410194 H3K4me3: Merck Millipore 07-473 For both ChIP and RNA-Seq experiments, cells were treated with compounds for 5 days. Followings are the final concentrations used: SGC-CBP30: 0.5 µM I-CBP112: 1 µM A485: 1 µM