Fig. 3. Modeling H3K27 methylation at PRE-equipped genes.

(A) Theschematic of tethered methylation subprocess of the simulation algorithm. During each inspection, it checks whether a nucleosome is engaged with a PRE-tethered PRC2 and increases the methylation probability accordingly. (B) The H3K27me3 distribution over the bithorax complex forecasted by the model is juxtaposed with distributions derived from two different ChIP-seq experiments (17, 39). Here and in (C), the simulated profiles show mean values from five inspections within one cell cycle over 1000 parallel simulations. The profiles derived from experimental measurements show mean ChIP-seq reads over a nucleosome. (C) The H3K27me3 (17, 39) and RNA-seq profiles (17, 40) over the erm locus. The dashed lines mark the edges of transcriptionally active regions. (D) Box plots of Jaccard indices comparing H3K27me3-enriched regions defined from experimental and simulation replicates (green), individual simulations and experiments (light blue), and between different experiments (dark blue). Note that simulations are less noisy and identify H3K27me3-enriched regions with precision comparable to that of the ChIP-seq assays.