The following new paper is posted in arxiv.
When bifunctional transcription factors activate and repress target genes within the same cell, these opposing activities must be encoded in regulatory DNA. Here, we use cellular resolution gene expression data and computational modeling to investigate Hunchback (Hb) bifunctionality in Drosophila embryogenesis. Previous computational models predicted that Hb both activated and repressed the enhancer controlling even- skipped (eve) stripes 3 and 7 (eve3+7). We tested this hypothesis by measuring and modeling eve expression under multiple genetic perturbations and found that the eve3+7 enhancer could not explain endogenous stripe 7 behavior. To explain this discrepancy, we measured the response of an extended eve stripe 2 enhancer that drives expression of eve stripes 2 and 7 (eve2+7). We found that the behavior of endogenous stripe 7 is explained by the combined behavior of both enhancers, eve3+7 and eve2+7. Bifunctionality arises from Hb activating the eve2+7 enhancer and repressing the eve3+7 enhancer. This pair can thus be considered “shadow enhancers” that both direct eve stripe 7, but respond to Hb in opposite ways. This example may illustrate a general way of encoding bifunctional regulation in the genome.