TABLE 2.
Average kinetic parameters (day−1) determined from fits of differential equations to the relative levels of various methylation species
Parameters are the rate of histone binding chromatin (α), labeled (k0→1, k1→2, k2→3) or unlabeled (k′0→1, k′1→2, k′2→3) methylation, demethylation (k3→2, k2→1, k1→0), and fragment degradation for each methylation state (μ0, μ1, μ2, μ3). All four μ parameters already account for dilution and thus represent degradation above the dilution rate. Parameters for H3K36 and H3K27 were determined with peptides in which the other residue (H3K27 and H3K36, respectively) on the same fragment was unmodified, because of the inability to localize the label on certain labeled intermediates, as detailed in Supplemental Table S1. Averages and standard deviations (parentheses) were taken for fits with an RMSD less than 125% of the minimum RMSD determined.
| H3K4 | H3K18 | H4R3 | H1.4K26 | H3K36 | H3K79 | H3K9 | H3K27 | H4K20 | |
|---|---|---|---|---|---|---|---|---|---|
| α | 0.6948 (0.0016) | 1.4611 (0.2633) | 1.9590 (1.1634) | 2.8488 (1.0027) | 0.2539 (0.0750) | 0.7088 (0.0977) | 0.9453 (0.2226) | 0.3848 (0.0540) | 0.8118 (0.1372) |
| k0→1 | 0.0939 (0.0016) | 0.0052 (0.0008) | 0.0117 (0.0015) | 0.0223 (0.0010) | 3.4092 (0.4868) | 0.1186 (0.0077) | 3.8746 (0.1482) | 7.0139 (0.0720) | 3.4327 (0.1048) |
| k1→2 | – | – | – | – | 5.4056 (0.0277) | 0.2177 (0.0099) | 2.2240 (0.0038) | 4.1676 (0.0070) | 1.4813 (0.0123) |
| k2→3 | – | – | – | – | – | – | 0.2676 (0.0003) | 0.2329 (0.0014) | 0.0000 (0.0000) |
| k′0→1 | 0.0200 (0.0007) | 0.0023 (0.0004) | 0.0019 (0.0006) | 0.0045 (0.0006) | 0.3104 (0.0520) | 0.0447 (0.0055) | 0.4320 (0.0229) | 1.0496 (0.0198) | 0.2212 (0.0186) |
| k′1→2 | – | – | – | – | 0.3323 (0.0194) | 0.0004 (0.0050) | 0.2043 (0.0016) | 0.0302 (0.0097) | 0.0039 (0.0118) |
| k′2→3 | – | – | – | – | – | – | 0.0531 (0.0007) | 0.0852 (0.0048) | 0.1603 (0.0133) |
| k1→0 | 0.0009 (0.0052) | 0.4943 (0.0188) | 0.1249 (0.1279) | 0.0401 (0.0422) | 1.2228 (0.4952) | 0.0125 (0.0308) | 0.2480 (0.2283) | 0.0016 (0.0084) | 0.0061 (0.0274) |
| k2→1 | – | – | – | – | 0.2510 (0.0455) | 0.0008 (0.0018) | 0.1020 (0.0016) | 0.0635 (0.0022) | 0.0703 (0.0038) |
| k3→2 | – | – | – | – | – | – | 0.0000 (0.0009) | 0.1680 (0.0101) | 6.9116 (1.2521) |
| μ0 | 0.0001 (0.0003) | 0.7704 (0.2633) | 1.2807 (1.1787) | 2.2330 (1.0385) | 3.2997 (1.7333) | 0.0171 (0.1193) | 0.6811 (1.1148) | 1.8727 (1.4989) | 0.7828 (0.8591) |
| μ1 | 0.0031 (0.0119) | 0.2834 (0.2406) | 0.1208 (0.0906) | 0.0374 (0.0315) | 2.6177 (1.2729) | 0.0221 (0.0447) | 0.7617 (0.2429) | 0.0047 (0.0396) | 0.0075 (0.0346) |
| μ2 | – | – | – | – | 0.3448 (0.0929) | 0.0061 (0.0476) | 0.0008 (0.0032) | 0.0000 (0.0007) | 0.0017 (0.0080) |
| μ3 | – | – | – | – | – | – | 0.0001 (0.0007) | 0.0003 (0.0045) | 0.2931 (0.4585) |