1. 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

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

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

4. CS1 CS2 CS3 CS4 Ambiguous Supplementary Figure 4 Domain length (kb) 1010 20
>26
Domain length (kb)

5. 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

6. 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

7. 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%)

8. 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