Rearrangements of 2.5 Kilobases of Noncoding DNA from the <em>Drosophila even-skipped</em> Locus Define Predictive Rules of Genomic <em>cis</em>-Regulatory Logic

<div><p>Rearrangements of about 2.5 kilobases of regulatory DNA located 5′ of the transcription start site of the <i>Drosophila even-skipped</i> locus generate large-scale changes in the expression of <i>even-skipped</i> stripes 2, 3, and 7. The most radical effects are generated by juxtaposing the minimal stripe enhancers MSE2 and MSE3 for stripes 2 and 3 with and without small “spacer” segments less than 360 bp in length. We placed these fusion constructs in a targeted transformation site and obtained quantitative expression data for these transformants together with their controlling transcription factors at cellular resolution. These data demonstrated that the rearrangements can alter expression levels in stripe 2 and the 2–3 interstripe by a factor of more than 10. We reasoned that this behavior would place tight constraints on possible rules of genomic <i>cis</i>-regulatory logic. To find these constraints, we confronted our new expression data together with previously obtained data on other constructs with a computational model. The model contained representations of thermodynamic protein–DNA interactions including steric interference and cooperative binding, short-range repression, direct repression, activation, and coactivation. The model was highly constrained by the training data, which it described within the limits of experimental error. The model, so constrained, was able to correctly predict expression patterns driven by enhancers for other <i>Drosophila</i> genes; <i>even-skipped</i> enhancers not included in the training set; stripe 2, 3, and 7 enhancers from various Drosophilid and Sepsid species; and long segments of <i>even-skipped</i> regulatory DNA that contain multiple enhancers. The model further demonstrated that elevated expression driven by a fusion of MSE2 and MSE3 was a consequence of the recruitment of a portion of MSE3 to become a functional component of MSE2, demonstrating that <i>cis</i>-regulatory “elements” are not elementary objects.</p>