Building blocks of the histone modification spreading and pattern formation model. (A) The nucleosome model consists of an array of 50 nucleosomes with one specific initiation site for the methyl- and acetyltransferases (indicated by the arrow). In (B) the nucleosome modification reactions are depicted, while (C-E) indicate the binding and movement properties of the transferase. (B) The nucleosomes can be in three modification states: A (acetylated; green star), U (unmodified), or M (methylated; red pentagram). The methyltransferase can bind to a nucleosome in any modification state but can catalyze only the reaction from U to M. Both the acetylation reactions, the conversion of U to A, and the demodification reactions from both A and M to U are ubiquitous and independent of the presence of the methyltransferase. Dashed arrows represent the binding of the transferase to the nucleosome. Binding of a transferase to a nucleosome occurs either by binding at the initiation site, by 1D diffusion, or by the recruitment process. (C) 1D diffusion of the transferase over the array in hops of one nucleosome. The transferase exclusively enters the nucleosome array at the specific initiation site (yellow) and has at each position equal chance to move left or right. Both the binding and diffusion reactions are independent of the modification state of the nucleosomes. The transferases cannot move over a neighboring transferase or a boundary. (D) Modification-induced transferase recruitment. The transferase lands on the initiation site (yellow) independent of the modification state of the nucleosome and can methylate the bound nucleosome and its neighbors. Methylated nucleosomes can recruit additional transferases. (E) Combined diffusion and modification-induced transferase recruitment. This mechanism combines all the characteristics of the two single movement mechanisms. Reactions are given in Additional file 10: S5.