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A Simple Histone Code Opens Many Paths to Epigenetics

Figure 3

Analysis of the 202 bistable E-opposite/R-out circuits.

These circuits have , and . (A) The table shows total numbers of each reaction among the 202 circuits, with types of reactions color-coded. These data are summarized in the circuit, where reaction frequency is denoted by arrow thickness. (B) Number of circuits with the indicated number of recruitment links in which E1 or E2 stimulates moves towards themselves (reactions 1, 2, 3, 6 by E1; 4, 5, 7, 8 by E2). (C) Number of circuits with the indicated number of recruitment links in which E1 or E2 stimulates moves away from themselves (reactions 4, 5, 7, 8 by E1; 1, 2, 3, 6 by E2). (D) Number of recruitment reactions per circuit. (E) Minimal number of recruited enzymes needed for the circuit. This is less than the number of recruitment reactions because in some cases the recruited enzyme acts to modify or de-modify a particular histone position without being sensitive to the modification state of the other position. For example, the consensus motif (Fig. 2A) has 8 recruitment reactions but only requires 4 enzymes. (F) Upper panel: Numbers of circuits with 0, 1 or 2 standard two-step positive feedback pathways stimulated by either E1 or E2 according to whether the pathway is over the R-state, or the non-R state. For example, the ‘classical’ circuit and the ‘reverse classical’ circuit are in the 44 and 12 member classes, respectively. Lower panel: Includes only standard 2-step pathways in which a recruited enzyme catalyzes conversion of the intermediate type to the opposing E type. Most standard two-step pathways are of this type.

doi: https://doi.org/10.1371/journal.pcbi.1002643.g003