Fig. 3: Transcription of housekeeping genes is affected in DomKD embryos.

a Violin plot showing the differential gene expression (DGE) as log2FoldChanges in gene expression of Ctrl vs DomKD in Zld-dependent, H2A.Z positive and H2A.Z negative genes measured by GRO-seq. See also Supplementary Fig. 3j. n = 3 biologically independent experiments per genotype. b Violin plot of the log2FoldChange for Pol II occupancy (Rpb3 ChIP-seq) per unique promoter of Zld-dependent, H2A.Z positive and H2A.Z negative promoters. See also Supplementary Fig. 3i. n = 2 biologically independent experiments per genotype. a, b All groups are significantly different by pairwise comparison, Wilcoxon rank sum test with continuity correction, two-sided, p-value < 2.2e–16. Box plots (a, b) depict the median and the interquartile range (IQR) from the 1^st to the 3^rd quartile. Whiskers indicate the upper (Q3 + 1.5*IQR) and lower edge (Q1 − 1.5*IQR). c Motif enrichment analysis of core promoter elements in Zld-dependent (Zld-dep), H2A.Z positive (H2A.Z pos) and H2A.Z negative (H2A.Z neg) promoters. d Gene set enrichment analysis using Metascape⁵⁶ showing the top 5 most significant GO terms per group (Zld-dep, H2A.Z pos and H2A.Z neg). Each GO-term is supported by the color scale in -log10 q-value and the fraction of observed genes presenting the proportion of observed genes in the respective GO term. Data representation was arranged as proposed by ref. ¹¹⁵. See also Supplementary Fig. 3l. c, d Source data are provided as a Source Data file.