Fig. 1.

Characterisation of pCRMs instructing ZGA. a Timeline (hpf, hours post-fertilisation, at 25 °C) of the maternal-to-zygotic transition and earliest signalling events (nuclear accumulation of Wnt, Nodal and Bmp signal mediators β-catenin, Smad2 and Smad1, respectively) during early X. tropicalis development up to the late gastrula embryo (12 hpf) with ∼40,000 (40 K) cells. b Signal transduction pathway causing signal mediators to enter the nucleus and engage with pCRMs (e.g., marked by RNAPII). c Snapshot of RNAPII recruitment to pCRMs of the zygotic gene locus tbxt from the 32-cell to the late gastrula stage. The underlying DNA sequence of RNAPII⁺ pCRMs are used to discover enriched DNA motifs de novo (illustrated as coloured arrows for one RNAPII⁺ pCRM). d Spearman correlations (R_s) of RNAPII binding levels across ∼27,000 pCRMs (Supplementary Data 2) between the indicated developmental stages. e Temporal enrichment (Z-score) of consensus DNA motifs known to be recognised by indicated TF families among RNAPII⁺ pCRMs. f MBT-staged heat map of DNase-probed chromatin accessibility, RNAPII binding and H3K4me1 marking (n = 2 biologically independent samples) across ∼17,500 pCRMs (Supplementary Data 3) grouped by sequence conservation levels (phastCons) and sorted by the statistical significance of pCRM accessibility. Abbreviations used for the developmental timeline: 32, 128 and 1 K, 32-, 128- and 1024-cell stage; MBT, mid-blastula transition; eG, mG and lG, early, mid- and late gastrula stage