Fig. 4

DV enhancers are primed by increased chromatin accessibility and CBP-mediated histone acetylation prior to the induction of DV transcription. a Schematic of the developmental stages profiled by ATAC-seq [36], ChIP-seq [57], and CUT&Tag (this study). b Boxplots of ATAC-seq enrichment (log₂ TPM) at DV and non-DV enhancers and promoters, relative to shuffled genomic regions from wild-type embryos at nc 11, 12, and 13. Significant differences (Wilcoxon rank-sum test) are indicated by asterisks, * = P < 0.05, ** = P < 0.01, *** = P < 0.001. c Overlap (%) of DV and non-DV enhancers and promoters with Zld ChIP-seq peaks from nc 8, 13, and 14 wild-type embryos [58]. d Boxplots showing the log₂ fold change (perturbation/control) in ATAC-seq signal at DV, non-DV, and shuffled enhancers and promoters after maternal RNAi depletion of zld and opa [59], CLAMP [60], and zygotic GAF^deGradFP [61]. P-values (Wilcoxon rank-sum test) show significant differences in accessibility compared to shuffled sites. e Overlap (%) of DV and non-DV enhancers and promoters with ChIP-seq peaks (nc 8, 12, 14 (early and late)) for the p300/CBP-mediated histone acetylation marks (H3K27ac, H3K18ac, and H4K8ac) and the non-p300/CBP mark H3K9ac [57]. f–i Metagene plots of (f) CBP-catalyzed histone marks from nc 8 ChIP-seq and g CBP CUT&Tag and ATAC-seq enrichment at DV enhancers acetylated or non-acetylated at nc 8. h Boxplots of 2.5–3 h and 4.5–5 h (AEL) PRO-seq gene body read counts (log₂) for DV genes linked to enhancers acetylated or non-acetylated at nc 8. P-values are from the Wilcoxon rank-sum test. i Metagene plots of BRD4/fs(1)h and Cdk9 CUT&Tag signal from nc 7–9, 11–13, and 14 wild-type embryos at the promoters of DV genes linked to enhancers acetylated or non-acetylated at nc 8