Supplementary Figure 1 K C H3K4me2 H3K4me3 H3K36me3 H2Bub H3K9me3

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Supplementary Figure 1 K C H3K4me2 H3K4me3 H3K36me3 H2Bub H3K9me3 H3K56ac H3K27me3 H3K27me2 H3K27me1 H3K9me2 H4K20me1 5mC H3 2.5 5 7.5 10 12.5 15 17.5

Supplementary Figure 2 Heterochromatic knob H3 H3K4me2 H3K4me3 H2Bub 5mC mRNA Chromatin states Genes H3K36me3 H3K56Ac H3K9me3 H3K27me3 H3K27me2 H3K27me1 H3K9me2 H4K20me1 Transposable elements

A B Supplementary Figure 3 % of observed combinations % of tiles per combination Number of tiles associated with each combination

CS1 CS2 CS3 CS4 Ambiguous Supplementary Figure 4 Domain length (kb) 10 10 20 >26 Domain length (kb)

Supplementary Figure 5 α H3K27me2 α H3K9me3 H3K27me2 peptide H3K27me1 0 mg 0.1 mg 1 mg 10 mg α H3K9me3 H3K9me3 peptide H3K36me3 0 mg 0.1 mg 1 mg 10 mg

Supplementary Table I Chr4 H3 H3K4me2 H3K36me3 H2Bub H3K56ac H3K4me3 5mC H3K9me2 H4K20me1 Genomic space covered (bp) Total 1.85E+07 1.62E+07 1.09E+07 6.51E+06 5.72E+06 4.90E+06 4.26E+06 3.88E+06 3.84E+06 7.92E+06 5.33E+06 6.68E+06 4.32E+06 3.16E+06 Euchromatin 1.55E+07 1.35E+07 1.08E+07 6.42E+06 5.66E+06 4.81E+06 4.08E+06 3.76E+06 3.79E+06 5.26E+06 2.66E+06 4.24E+06 1.58E+06 8.47E+05 Heterochromatin 3.05E+06 2.63E+06 1.81E+05 9.93E+04 6.13E+04 9.06E+04 1.78E+05 1.27E+05 5.49E+04 2.68E+06 2.44E+06 2.73E+06 2.32E+06 Relative distribution over Chr4 (%) 83.6 73.1 58.1 34.6 30.5 25.9 22.0 20.3 20.4 28.4 14.3 22.9 8.5 4.6 16.4 14.2 1.0 0.5 0.3 0.7 14.4 13.1 14.7 12.5 Relative coverage (%) 100.0 87.5 69.5 41.4 36.5 31.0 26.4 24.3 24.5 33.9 17.2 27.4 10.2 5.5 86.3 5.9 3.3 2.0 3.0 5.8 4.2 1.8 87.4 87.8 79.9 89.7 76.1 Relative distribution between compartments (%) 83.7 98.4 98.5 98.9 98.2 95.8 96.7 98.6 66.4 49.8 63.5 36.7 26.7 16.3 1.6 1.5 1.1 1.4 33.6 50.2 63.3 73.3

Median length of marked domains in euchromatin (bp) Supplementary Table II H3 H3K4me2 H3K4me3 H3K36me3 H3K56ac H3K9me3 H2Bub H3K27me3 H3K27me2 H3K27me1 H3K9me2 H4K20me1 5mC Nb of marked domains ND 898 1163 1042 1122 1000 838 638 908 610 306 337 Median length of marked domains in euchromatin (bp) 7272 2804 4527 3242 2995 4816 4283 4053 3109 3455 2461 1873 Nb of marked genes (total=4103) 3890 (95%) 3646 (87%) 2136 (52%) 2432 (59%) 2319 (57%) 1643 (40%) 2048 (50%) 1190 (29%) 1472 (36%) 704 (17%) 242 (6%) 182 (4%) 1574 (38%) Nb of marked TEs (total= 3191) 2605 (82%) 293 (9%) 82 (3%) 72 (2%) 108 62 39 (1%) 523 (16%) 2473 (77%) 1859 (58%) 2143 (67%) 1387 (43%) 1866 (58%)

Supplementary Table V All Tiles Genic Tiles H3K4me2 H3K4me3 H3K9me2 H3K56ac 5mC H4K20me1 H2Bub H3K27me1 0.93 0.09 0.96 0.35 0.54 0.97 0.43 0.18 0.94 0.31 0.34 0.03 0.66 0.06 0.67 0.10 0.05 0.46 0.04 0.47 0.08 0.02 0.51 0.85 0.32 0.62 0.57 0.56 0.24 0.11 0.82 0.69 0.19 0.55 0.87 0.20 0.07 0.37 0.86 0.75 0.38 0.73 0.12 0.15 0.72 0.30 0.45 0.17 0.76 0.33 0.61 0.63 0.40 0.49 0.88 0.77 0.84 0.13 0.81 All Tiles Genic Tiles H3K4me2 H3K4me3 H3K9me2 H3K9me3 H3K27me2 H3K27me3 H3K36me3 H3K56ac 5mC H4K20me1 H2Bub H3K27me1 0.95 0.25 0.98 0.53 0.56 0.97 0.96 0.69 0.50 0.64 0.34 0.05 0.66 0.08 0.06 0.54 0.67 0.16 0.12 0.47 0.03 0.02 0.22 0.07 0.23 0.58 0.36 0.33 0.61 0.04 0.29 0.20 0.57 0.10 0.75 0.68 0.19 0.32 0.70 0.55 0.18 0.11 0.87 0.76 0.51 0.27 0.37 0.73 0.17 0.44 0.15 0.60 0.30 0.59 0.43 0.45 0.89 0.77 0.13 0.52