Fig. 2

Epigenomic profiling identifies chromatin states at DV enhancers and promoters that correlate with tissue-specific gene expression. a Schematic of the epigenomic profiling strategy for identifying tissue-specific DV enhancers genome-wide. PRO-seq identified DV genes were linked to regions within the same topologically associating domain (TAD) with differential chromatin accessibility (ATAC-seq), enrichment of the active histone mark H3K27ac, and occupancy of CBP between Toll mutants. b The fold change (log₂) in ATAC-seq and CBP and H3K27ac [9, 14, 15] ChIP-seq tissue-specific enrichment scores from Toll mutant embryos at DV (dorsal ectoderm n = 72, neuroectoderm n = 51, mesoderm n = 53) and non-DV (n = 9383) enhancers. Significant differences in enrichment from the Wilcoxon signed-rank test are indicated by asterisks, * = P < 0.05, ** = P < 0.01, *** = P < 0.001. c Correlations of the combined tissue-specific enhancer chromatin state score and target DV gene tissue-specific transcription. The coefficient of determination (R²) is shown alongside asterisks denoting the associated P-value significance, * = P < 0.05, ** = P < 0.01, *** = P < 0.001. d The fold change (log₂) in tissue-specific enrichment scores from Toll mutants for the genomic datasets in b at promoters associated with DV enhancers (dorsal ectoderm n = 41, neuroectoderm n = 29, mesoderm n = 37). e Correlations of the combined tissue-specific promoter chromatin state score and target DV gene tissue-specific transcription. f Genome browser shots of Toll mutant ATAC-seq (3, 4, and 5 h AEL), H3K27ac and CBP ChIP-seq (2–4 h AEL) and PRO-seq (3 h) alongside Dl ChIP-nexus (2–4 AEL wild-type embryos) [33] at dpp, ind, and twi. The genomic position of DV enhancers and promoters are denoted. g Boxplots showing the fold change (log₂) in enhancer RNA (eRNA) activity measured from Toll mutant PRO-seq at DV and non-DV enhancers. h Metagene profiles of Toll mutant PRO-seq (3 h) and Pol II (Rpb3) CUT&Tag (2–4 h AEL) signal (RPKM) at DV enhancers (± 5 kb of CBP) and promoters (± 5 kb of TSS)