Synthetic enhancers reveal design principles of cell state specific regulatory elements in hematopoiesis

Abstract During cellular differentiation, enhancers transform overlapping gradients of transcription factors (TFs) to highly specific gene expression patterns. However, the vast complexity of regulatory DNA impedes the identification of the underlying cis-regulatory rules. Here, we have characterized 62,126 fully synthetic DNA sequences to bottom-up dissect design principles of cell-state specific enhancers in the context of the differentiation of blood stem cells to seven myeloid lineages. Focusing on binding sites for 38 TFs and their pairwise interactions, we found that identical sites displayed both repressive and activating function, as a consequence of cellular context, site combinatorics, or simply predicted occupancy of a TF on an enhancer. Surprisingly, we found that combinations of activating sites frequently neutralized each other or even gained repressive function. These negative synergies convert quantitative imbalances in transcription factor expression into binary downstream activity patterns, a principle that can be exploited to build differentiation-state specific enhancers from scratch.