Table 3. Propensity functions used in the simulations.

Propensities
Non-assembly methylation propensity	$$\begin{gathered} {\displaystyle \begin{array}{l}{b}_i^{\text{me}}=\beta \left({\delta }_{{\mathrm{S}}_{\mathrm{i}},\mathrm{m}\mathrm{e}0}\left({\gamma }_{\text{me0-1}}+{\mathrm{k}}_{\mathrm{m}\mathrm{e}0-1}{\mathrm{E}}_{\mathrm{i}}\right)+{\delta }_{{\mathrm{S}}_{\mathrm{i}},\mathrm{m}\mathrm{e}1}\left({\gamma }_{\text{me1-2}}+{\mathrm{k}}_{\mathrm{m}\mathrm{e}1-2}{\mathrm{E}}_{\mathrm{i}}\right) \\ +{\delta }_{{\mathrm{S}}_{\mathrm{i}},\mathrm{m}\mathrm{e}2}\left({\gamma }_{\text{me2-3}}+{\mathrm{k}}_{\mathrm{m}\mathrm{e}2-3}{\mathrm{E}}_{\mathrm{i}}\right)\right)\end{array}} \end{gathered}$$
Demethylation propensity	$r_i^{\text{dem}}={\gamma }_{dem}({\delta }_{S_i\text{,me1}}+{\delta }_{S_i,\text{me2}}+{\delta }_{S_{i,}\text{me3}})$
Transcription	${\displaystyle f=\{\begin{array}{l}\alpha \left(f_{max}-\frac{P{\left(R_m\right)}_{me2/me3}}{P_T}\left(f_{max}-f_{min}\right)\right)\\ \alpha f_{min},P{\left(R_m\right)}_{me2/me3}\ge P_T\end{array},P{\left(R_m\right)}_{me2/me3}<P_T}$ ${\displaystyle m=\{\begin{array}{l}NR,P{\left(R_{NR}\right)}_{me2/me3}>P{\left(R_B\right)}_{me2/me3}\\ B,P{\left(R_{NR}\right)}_{me2/me3}\le P{\left(R_B\right)}_{me2/me3}\end{array}}$ ${\displaystyle \mathrm{i}\mathrm{f}f>f_{lim}\mathrm{t}\mathrm{h}\mathrm{e}\mathrm{n}f=f_{lim}}$
Protein binding propensity	${\displaystyle \begin{array}{l}\mathrm{I}\mathrm{f}Q<N_P\mathrm{t}\mathrm{h}\mathrm{e}\mathrm{n}{r}^{bind}={\gamma }_{bind}\left(w\right)+k_{bind}G\\ \mathrm{I}\mathrm{f}Q=N_P\mathrm{t}\mathrm{h}\mathrm{e}\mathrm{n}{r}^{bind}=0\end{array}}$
Protein unbinding propensity	$r_k^{unbind}={\delta }_{P_k,\mathrm{b}\mathrm{o}\mathrm{u}\mathrm{n}\mathrm{d}}{\gamma }_{unbind}$
Total methylation propensity	${\displaystyle r_i^{\text{me}}=\{\begin{array}{cc}{b}_i^{me}+k_{p-me}G\left({\delta }_{S_i,me0}+{\delta }_{S_i,me1}+{\delta }_{S_i,me2}\right),& i\in R_{NR}\\ b_i^{me},& i\in R_B\end{array}}$