Fig. 4

Analysis of key regulatory proteins and histone PTMs during JQ1 cell treatment. a (+)-JQ1 treatment of ESCs results in a decrease in Nanog-GFP as measured by FACS. b In triplicate experiments, ESCs were initiated into differentiation in medium lacking LIF. Matched cultures comprising DMSO control (-RA-JQ1), RA treatment for 6 days (+RA-JQ1), JQ1 treatment for 6 days (-RA + JQ1) and RA for 3 days followed by JQ1 for 3 days were maintained and for 6 days with media changes on alternate days. On harvest, mRNA abundance was analyzed by qPCR using a panel of primers (Additional file 1: Table S1). The DDCt data was represented as relative fold over DMSO control (-RA-JQ1). Expression of pluripotency markers, Oct4 and Nanog decreases upon RA and (+)-JQ1 treatment as compared to DMSO control without drug, while expression of germ layer markers increased. The trends of differentiation by inhibition of BET domain by these two treatments and a combination thereof are shown as averages (bottom cells) of multiple markers, respectively for endoderm and neurectoderm. c Most significant histone PTM changes during inhibitor treatment. d Representation of all histone PTMs by plotting their log2 fold change between untreated cells and treated with 100 nM (left) or 200 nM (right) of JQ1 inhibitor. Significant changes were considered when the–test p-value (homoscedastic, two tails) was <0.05, equivalent to >4.32 when transformed into–log2. Color code represents different histone modification types. e Representation of all histone peptide regulations in cells untreated vs treated with JQ1. The two different doses were marked with black and red dots. The figure displays a tight correlation of histone peptide regulation between the two treatments