Fig. 5 | Nature Communications

Fig. 5

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

Fig. 5

Reconciling bivalent and bistable chromatin. a Previous models propose that bivalent chromatin, containing H3K27me3 and H3K4me3, is poised for activation or silencing in pluripotent cells, and is resolved to an active or silent state upon differentiation. b We propose that the poised, pluripotent state is bistable, not bivalent. c Dynamic bistability. In the model, in active chromatin, nucleosomes switch dynamically between fully active and active bivalent configurations. In silent chromatin, nucleosomes alternate between fully silent and silent bivalent configurations. d Schematic time course plots of bistable model in different modes. Crosslinking window: a ChIP experiment can capture bistable chromatin in different states in different cells and will thus represent a mixture of the active and silent states. e Predictions of the bistable model for a single locus. The model predicts that distinct types of bivalent nucleosomes co-occur with active or silent chromatin. f Single ChIP and population mRNA analysis would give identical results for both the bivalent and bistable models. g, h Re-ChIP (i.e. sequential or concurrent ChIP with two antibodies) and single-cell mRNA analysis would give different results under the bivalent (g) and bistable (h) models. i Epigeneticist landscape. Citation frequency for each of the 12 half-nucleosome states shown in Fig. 1d is plotted as – log of total citations of original publications that address a state or transition (see “Methods” section for details and literature). Rarely cited and less abundant publications are shaded light and occur on the hills. Highly cited publications are shaded dark and occur in the valleys. Publications relating to silent or bivalent states that contain H3K27me3 (half-nucleosome states 9–12) are the most abundant and highly cited. j For comparison, a similar landscape plotting – log of average occupancy of each of the 12 half- nucleosome states under bistable conditions as in Fig. 3b. Rare states are shaded light and occur on the hills. Frequently occurring states are shaded dark and occur in the valleys. The density of research relating to each state is disproportionate to the predicted occurrence of each in the model system

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