Genome-wide profiles of chromatin accessibility in spatially-restricted domains along the antero-posterior axis of Drosophila blastoderm

Establishment of spatial coordinates during early Drosophila embryogenesis relies on differential activity of axis patterning enhancers. Concentration gradients along the embryonic axes of activator and repressor transcription factors (TFs) provide positional information to each enhancer, which in turn promotes transcription of a target gene in a specific spatial pattern. In order to receive the TF input, an enhancer must be accessible. However, the interplay between an enhancer regulatory activity and its accessibility as determined by local chromatin organization in not well understood. Notably, it is unclear whether chromatin organization of axis patterning enhancers is uniform across the embryo or varies regionally with their differential activity. We profiled chromatin accessibility with ATAC-seq in narrow, genetically tagged domains along the antero-posterior (AP) axis in the Drosophila blastoderm. In a series of transgenic strains, we drove expression of a nuclear tag (nuclear-envelope marker UNC84-3xFLAG) under control of well-characterised enhancers of the AP gene regulatory network. Tagged nuclei were subsequently isolated from the whole-embryo homogenate by anti-FLAG antibody pull-down, followed by Tn5 transposase digestion of the native chromatin (ATAC-seq). We demonstrate that one quarter of the accessible genome displays significant regional variation in its ATAC-seq signal immediately after zygotic genome activation. Axis patterning enhancers are enriched among the most variable regions and their accessibility changes correlate with their regulatory activity. When receiving a net activating input and promoting transcription, an enhancer displays elevated accessibility in comparison to the region of the embryo where it receives a net repressive input. ATAC-seq was performed on tagged nuclei from seven domains (D1-D7) along the AP axis of stage-5 Drosophila melanogaster blastoderm. Spatial positions of these domains were defined by expression of a nuclear tag under control of well-characterized enhancers of early blastoderm genes (D1: hunchback anterior domain; D2: even-skipped stripe 2; D3: even-skipped stripe 1; D4: Dichaete central domain; D5: Kruppel central domain; D6: even-skipped stripe 5; D7: giant posterior domain). All transgenic strains were generated in the wild-type background. Each domain was assayed in duplicates that represented independent transgenic strains with the same expression construct. As a control, ATAC-seq was performed on the entire pool of nuclei from selected transgenic strains (referred to as whole-embryo controls; performed in duplicates). Additionally, ATAC-seq performed on purified genomic DNA was used as a reference for peak calling (gDNA sample).