ChIP-seq of ZGA staged embryos

During embryogenesis, the genome shifts from transcriptionally quiescent to extensively active in a process known as Zygotic Genome Activation (ZGA). In Drosophila, the pioneer factor Zelda is known to be essential for the progression of development, still, it regulates the activation of only a small subset of genes at ZGA. However, thousands of genes do not require Zelda, suggesting that other mechanisms exist. By conducting GRO-seq, HiC and ChIP-seq in Drosophila embryos, we demonstrate that up to 65% of zygotically activated genes are enriched for the histone variant H2A.Z and independent of Zelda. H2A.Z enrichment precedes ZGA and Polymerase II loading onto chromatin. In vivo knock-down of maternally contributed Domino, a histone chaperone and ATPase, reduces H2A.Z deposition at transcription start sites, causes global downregulation of housekeeping genes at ZGA, and compromises the establishment of the 3D chromatin structure. We infer that maternal factors and H2A.Z are master regulators of the de novo establishment of transcriptional programs during ZGA via chromatin reorganization. Corresponding inputs and ChIP-seqs of H2A.Zand Rpb3 in pre-ZGA embryos(c9-13), 2 replicates per stage. Corresponding inputs and ChIP-seqs of H2A.Z and Rpb3 in ZGA embryos in Ctrl and DomKD embryos, two replicates per condition. Corresponding inputs and ChIP-seq of H3K4me3 and H3K36me3 in ZGA Ctrl embryos, 2 replicates each.