From our analysis we also observed that Bptf-dependent gene targets are more likely to be actively regulated genes, repressed in the presence of LIF or RA differentiation and conversely activated under conditions of LIF differentiation (Figure S20A, S20B, S20C). In support with these observations we observed histone modifications in Bptf knockout ES cell lines consistent with a repressed transcriptome under LIF+ growth conditions (Figure S20D). Interestingly some Bptf-dependent genes cluster together in the genome (Figure S21).
