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. Author manuscript; available in PMC: 2017 Jul 7.
Published in final edited form as: Natl Sci Rev. 2016 Apr 19;3(2):240–251. doi: 10.1093/nsr/nww025

Figure 6.

Figure 6

Illustration of incorporating DNA accessibility in thermodynamics model. It shows the major components of transcriptional regulation and their interactions in thermodynamic equilibrium. A simplified transcriptional system where the enhancer contains a single binding site for a TF, with the TF bound or not bound at its site and the RNAP bound or not bound at the promoter. Arrows indicate TF-DNA, RNAP-DNA, and TF-RNAP interactions. Thermodynamics model allows us to predict the level of gene expression in the dynamical system by modeling the energies associated with these interactions. Considering the DNA accessibility of those regulatory elements, one can quantitatively describe the TF-DNA binding energy at functional regions changes according to the open chromatin state.