The cis-regulatory dynamics of embryonic development at single cell resolution

Single cell measurements of gene expression are providing new insights into lineage commitment, yet the regulatory changes underlying individual cell trajectories remain elusive. Here, we profiled chromatin accessibility in over 20,000 single nuclei across multiple stages of Drosophila embryogenesis. Our data reveal heterogeneity in the regulatory landscape prior to gastrulation that reflects anatomical position, a feature that aligns with future cell fate. During mid embryogenesis, tissue granularity emerges such that cell types can be inferred by their chromatin accessibility, while maintaining a signature of their germ layer of origin. We identify over 30,000 distal elements with tissue-specific accessibility. Using transgenic embryos, we tested the germ layer specificity of a subset of predicted enhancers, achieving near-perfect accuracy. Overall, these data demonstrate the power of shotgun single cell profiling of embryos to resolve dynamic changes in open chromatin during development, and to uncover the cis-regulatory programs of germ layers and cell types. Overall design: sci-ATAC-seq data was collected on whole Drosophila embryos collected from 3 time points - 2 to 4 hours after egg laying (AEL), 6 to 8 hours AEL, and 10 to 12 hours AEL). In total, we collected data on 23,086 individual cells. Custom scripts for processing data are available at https://github.com/shendurelab/fly-atac. This series includes bulk DNAse-seq samples from wildtype, elav+, or Mef2+ 6-8 hr embryonic nuclei.