Fig. 3 | Nature Communications

Fig. 3

From: Theoretical analysis of Polycomb-Trithorax systems predicts that poised chromatin is bistable and not bivalent

Fig. 3

The model adopts active, silent, or bistable modes. ac Simulated time course of dynamics of a system of N = 20 half nucleosomes with 2-fold variation in the rate of removal of H3K27ac by NURD. For all three plots, the rate of all transitions in the model is 1.0, with the exception of NURD as indicated, beta = 0.1, and PR-DUB = 0.15. Time is measured as number of recruitment attempts per half-nucleosome (see “Methods” section for more detail). Y-axis shows proportion of whole nucleosomes in each of categories 1–5, according to the colour scale given on the bottom right of the figure. df Time-averaged landscapes for the three cases, shown in terms of the probability to find a whole-nucleosome in any of the 144 modification states, averaged over a simulation of 50,000 time units. Half- and whole-nucleosome modification states are arranged and colour coded as in Fig. 2b. The vertical scale gives average proportion of whole array in a given modification state. e The bistability shown in (b) is reflected in the two peaks at the extreme corners of the landscape. gi The data from (d) to (f) are summarised in terms of total average occupation of each of categories 1–6. j System behaviour upon change in the rate constants NURD and PR-DUB with all other parameters fixed as in (af). Each simulation was performed for 50,000 time units and average system state over the entire time course was calculated. Red dots: category 5 (silent) dominates (average occupancy of category 5 nucleosomes larger than 50%). Green dots: category 1 (active) dominates. Note that all five modification categories were scored (see legend) but categories 2–4 did not dominate under any condition. Black circles: bistability, defined as multiple transitions between situations with more than 60% category 5 nucleosomes and those with more than 60% category 1 nucleosomes, each of which has an average lifetime of 40 time units. Grey arrows: positions for PR-DUB and NURD values as in (ai). k As for (j) but with replication at every 20 time units, simulated by resetting each half-nucleosome to the unmodified state with 50% probability

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