A fractional occupancy model learned different cooperative rules of TF binding that explain CRM penetrance and expressivity.

<p>(A) Red and blue bars represent the experimentally measured penetrance and expressivity, respectively, of the six-motif pMad-Tin heterotypic CRMs in the VM. Gray bars represent the model's fitted results when pMad-Tin-pMad cooperative interactions were included. (B–E) CRM activity for short pMad-Tin heterotypic CRMs. Double <i>in situ</i> hybridization against the <i>lacZ</i> reporter gene driven by the synthetic CRMs (B–E, red) and the endogenous <i>dpp</i> gene (B′–E′) green), where arrowheads indicate the midgut visceral mesoderm (VM). Embryos are dorsally oriented, with anterior to the left, stage 13/14. (B″–E″) Schematic representations of the CRM composition, where purple and green triangles depict the number and orientation of pMad or Tin sites, respectively. Spacing between adjacent pMad-Tin sites (below) and pMad-pMad sites (above) is indicated. (F) Penetrance (red bars) and expressivity (blue bars) of the short pMad-Tin heterotypic CRMs in the VM with the model's prediction (black bars) when pMad-Tin-pMad cooperative interactions were included. (G) Model predictions for pMad-Tin enhancers of different motif number with antisense orientation of the Tin site and 4 bp separation between sites. Red (blue) curve corresponds to the model prediction with (or without) pMad-Tin-pMad interactions. (H) As (A) but for the heart, where only non-zero results are shown. Note that we fit the heart data including the penetrance and expressivity results from the <i>P</i>-element pMad-Tin A2 line. Gray bars represent the model fit when considering Tin-pMad-Tin as the minimal cooperative TF configuration.