Extended Data Figure 3: Chromatin state distribution and positional preferences of regulatory binding.

a, Chromatin state distribution (y axis) of embryonic binding regions as a function of binding region occupancy (x axis). Embryonic binding regions with occupancies spanning 1–20 were mapped to 16 hierarchically linked infinite HMM (hiHMM) chromatin states¹⁴ discovered in embryos. Regulator binding regions (RGB)-, HOT-region and XOT-region occupancy levels are indicated along the x axis as blue, yellow and red bars, respectively. Chromatin state identities are indicated underneath. b, c, Fold change in frequency of chromatin states as a function of occupancy in embryos (b) and in L3 larvae (c). HOT and XOT cut-offs for each stage are indicated in dashed lines. d, e, Chromatin state distribution of factor binding in embryonic and larval L3 stages. Embryonic (d) and larval L3 (e) binding sites from individual ChIP-seq experiments were mapped to chromatin states derived from embryos and L3 larvae, respectively¹⁴. f, Signal densities near enzymatically-derived TSSs²⁹. The log₂ ratio of upstream (red) versus downstream (blue) binding is colour-coded below. Factors discussed in the text are highlighted.