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Figure 6 | BMC Biology

Figure 6

From: A framework for modelling gene regulation which accommodates non-equilibrium mechanisms

Figure 6

Formation of an inherently bounded chromatin domain [ [47],[48]]. (A) An array of nucleosomes is shown, with nucleation taking place at the right-hand end. White nucleosomes are unmarked, black nucleosomes are marked and grey nucleosomes are either marked or unmarked. Nucleation, at rate k+, is confined to the nucleation site; propagation, also at rate k+, allows a marked nucleosome to propagate the mark to one of its two immediate (unmarked) neighbours; turnover, at rate k_, allows any marked nucleosome, including the nucleation site, to become unmarked. (B) Directed graph for the model with three nucleosomes. Each microstate shows its marking pattern as a bit string with 0 denoting unmarked and 1 denoting marked. The microstates are enumerated by considering the bit string as a number in base 2 notation and adding 1. The edges correspond to nucleation, propagation and turnover, as above. Labels have been omitted for clarity but an edge that increases, respectively decreases, the number of bits has label k+, respectively k_. (C) On the left, an extension of the model to include mark stabilisation, with a stably marked nucleosome shown in magenta. A stabilised mark is no longer subject to turnover. This leads to the non-strongly connected graph shown on the right for an array of two nucleosomes, in which the digit 2 in the microstate description signifies a stabilised mark. Edges that change digit 1 to digit 2 have label k , while the other edges are labelled as in (B). The strongly connected components (SCCs) are indicated by dotted outlines, with the two terminal SCCs identified by an asterisk.

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