Quantitative modulation of a spatial enhancer through the biophysical properties of a transcription factor binding site

Fine-tuning of gene expression by transcription factors (TF) is essential
for normal development, but how TF binding is converted into precise
expression levels is poorly understood. We used a Drosophila enhancer
responding to the TF Distal-less (Dll) to investigate this relationship.
By combining computational structural analysis and quantifying relative
TFBS affinity and enhancer activity we describe how TF concentration is
converted into precise expression across developing Drosophila wings. We
show that the regulatory function of the enhancer closely follow the
classical Hill equation, and we describe the effects of affinity,
orientation, sequence and wing-region on the maximum achievable expression
and the position of transcriptional activity in a tissue. We also found
that Dll relies on two distinct sets of amino acid-DNA contacts for higher
affinity sites, but contacts are more evenly distributed at lower
affinities. Our work integrates information at molecular and tissue scales
to describe how the modulation of a single TF binding site determines the
regulatory function of an enhancer in a complex in vivo environment.