Figure 3. Binding behavior of MYC in U2OS cells analyzed by mathematical modeling.
(A) Schematic representation of model 1. For details see Appendix 1. (B, C) Plot illustrating regions of occupancy in the parameter space of dissociation constants KEbox and KNNNNNN as well as total amount of MYC. The grey area indicates the experimentally available concentration range, that is, EtOH to 1 µg/ml doxycycline (Dox) treatment. Regions of 1, 10, 50 and 90% occupancy of E-boxes (B) as well as 0.01% and 0.1% occupancy of NNNNNN sequences (C) are shown. The red line (B) and blue line (C) give the combination of the particular dissociation constants published by Guo et al. (2014). (D) Simulations show that occupancy of E-boxes (red line) by MYC is less than 10% in the measured range of MYC (grey area) while occupancy of NNNNNN (blue line) is below 1%. The EC50, which is the concentration of total MYC to obtain 50% occupancy, is calculated to be 1x102 μM for E-boxes. (E) The EC50 of E-boxes (1x102 μM estimated in D) can be reduced by decreasing the value of KEbox. Simulations predict that a reduction of KEbox (value published by Guo et al., 2014, is indicated by the dashed line) by about one order of magnitude already shifts the EC50 into the measured range of MYC (grey area). (F) Schematic representation of model 2. For details see Appendix 1. (G) In model 2, a reduction of the apparent dissociation constant of MYC and E-boxes as well as that of MYC and unspecific DNA sites are assumed by means of additional regulatory proteins such as WDR5. In the presence of WDR5, occupancy of E-boxes by MYC is above 95% (green line, EC50= 1.4x10-2 μM) and occupancy of unspecific DNA sites by MYC is above 50% (yellow line, EC50 =2.7x10–1 μM). Occupancy of E-boxes or unspecific DNA sites that are not bound by WDR5 (red and blue line, respectively) remain however below 10% and 1%, respectively, in the measured range of MYC (grey area).