Fig. 1 | Nature Communications

Fig. 1

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

Fig. 1

A comprehensive model of Polycomb/Trithorax regulation. a Left: The model considers four histone modifications catalysed by TrxG and PcG proteins. Middle: The model consists of an array of half-nucleosomes, each of which can carry one or more of these modifications, and are combined to give whole nucleosomes (see Fig. 2b). Right: the writers and erasers for each of these modifications are included in the model (see also Table 1). A simplified nomenclature is used throughout as indicated. TRXG indicates both H3K4 and H3K36 methyltransferases. KDM indicates both H3K4 and H3K36 demethylases. b There are 12 different possible modification states for each half-nucleosome (containing one copy of H3 and one of H2A), shown in a three-dimensional geometry. Adjacent states in horizontal and vertical directions are different from one another by one modification. Modifications in common for given half-nucleosome states are indicated. Grey arrows indicate the direction in which the system state is pushed by raising or lowering the activities of the complexes indicated. c Model logic. Half-nucleosome 1 is selected at random from the array, and recruits a complex (reader) depending on modifications. The recruited complex attempts to modify (write to) a second randomly selected half-nucleosome. d Full model. The diagram shown in (a) is viewed from above. Half-nucleosome states are numbered 1-12 with modifications as shown. Writers and erasers: Coloured arrows indicate transitions between half-nucleosome states for half-nucleosome 2. Red: towards silencing, green: towards activation. Complexes responsible for each transition are indicated on the arrows. Grey arrows: if the complex responsible for this transition is inhibited by an existing modification on half-nucleosome 2, the transition occurs only via the direct conversion parameter beta (see Methods). Readers: Complexes that can be recruited by half-nucleosome 1 in a given state are shown above each state, with red or green text indicating complexes that favour silencing or activation respectively. Compound complexes (e.g., TRXG:CBP) are included where evidence exists for physical interaction (see Methods and Tables 13 for details)

Back to article page