Cell
Design principles of cell-state-specific enhancers in hematopoiesis
Robert Frömel1,2 ∙ Julia Rühle1,2 ∙ Aina Bernal Martinez1 ∙ … ∙ Felix Pacheco Pastor1 ∙ Rosa Martinez-Corral3 ∙ Lars Velten1,2,4 et al
Highlights
• Cell-state-specific activity measurements of 64,400 minimalistic enhancers
• Individual transcription factors are often both activators and repressors
• Negative synergies between activators result in cell-state-specific repression
• Modeling enables the automated design of cell-type-specific enhancers in blood
Summary
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 characterized 64,400 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 cell state, site combinatorics, or simply predicted occupancy of a TF on an enhancer. Surprisingly, combinations of activating sites frequently neutralized one another or gained repressive function. These negative synergies convert quantitative imbalances in TF expression into binary activity patterns. We exploit this principle to automatically create enhancers with specificity to user-defined combinations of hematopoietic progenitor cell states from scratch.
