Genome-wide mapping of Bicoid/DNA interactions reveals quantitative constraints on transcriptional regulation

During Drosophila embryogenesis, Bicoid (Bcd) forms a gradient that provides positional information to regulate target genes along the anteroposterior axis. To understand how the information provided by the Bcd gradient drives gene expression in a concentration-dependent manner, the subpopulations of Bcd participating in gene regulation need to be characterized. Therefore, to understand the mechanism of Bcd-mediated gene regulation, we quantified the absolute concentration of the nuclear subpopulations of Bcd, such as freely diffusing, DNA bound, and clustered Bcd. Each of these populations have distinct diffusivities and DNA-binding properties and are proposed to be crucial for gene regulation. This quantification allowed us to construct a global dose/response relationship between the free and DNA-bound concentration of Bcd. Our data show that Bcd/DNA binding is strongly correlated with the free concentration of Bcd, indicated by the dose/response relationship being in the linear regime, despite the barrier presented by nucleosomes. Our data are quantitatively consistent with a Monod-Wyman-Changeux model in which transcription factors passively compete with nucleosomes for DNA binding. We further apply this model to Bcd/DNA interactions at the enhancer/promoter for hunchback (hb), a Bcd target gene which has a steep posterior boundary, despite being driven primarily by the graded Bcd concentration, a conundrum which has been under scrutiny for decades We show that, using parameters determined form the global dose/response relationship, a reversible multistate promoter model, in which the promoter activation rate is determined by Bcd binding to the hb enhancer, can successfully recapitulate features of hb transcriptional dynamics, including the sharp posterior boundary. Therefore, this work sheds light on mechanism of hb regulation by Bcd and provides a potential experimental/computational pipeline that bridges the input of global properties of transcription factors to the transcriptional output of specific target genes.