Thermodynamics-Based Models of Transcriptional Regulation by Enhancers: The Roles of Synergistic Activation, Cooperative Binding and Short-Range Repression
Figure 2
Effect of cooperative DNA-binding of TFs and the mode of transcriptional activation (multiplicative or not) on model performance.
(A,B) Predicted expression profiles of a DirectInt model with no cooperativity (“no-coop”, blue) and a model with self-cooperative binding for Bcd and Kni (“coop”, green) are shown for each CRM, with reference to the CRM's known readout (“Obs.”, red). The correlation coefficient between a model's prediction and the known readout is indicated in the top right corner of the panel. Each expression profile is on a scale of 0 to 1 (scaling does not affect correlation coefficient), and shown for bins 20 to 80 (i.e., 20% to 80% egg length) of the embryo. Shown are two CRMs for which one model was deemed better than the other (CC≥0.65, difference in CC≥0.05). (C,D) Predicted expression profiles of a DirectInt model with multiplicative activation (“synergy”, green) and one with additive activation (“no-synergy”, blue). Shown are two CRMs where the multiplicative model is better than the additive model (CC≥0.65, difference in CC≥0.05). Self-cooperative DNA-binding was not used in this evaluation.