Expression profiling by high throughput sequencing
Drosophila melanogaster is a powerful, long-standing model for metazoan development and gene regulation. We profiled chromatin accessibility in almost one million, and gene expression in half a million, nuclei from eleven tightly staged, overlapping windows of its embryogenesis. Leveraging the asynchronicity of embryos within each collection, we developed a statistical model to more precisely estimate the age of each nucleus, resulting in continuous views of molecular and cellular transitions throughout the majority of embryonic development. From these data, we identify cell types, infer their developmental relationships, and link cell type-specific changes to dynamic changes in enhancer usage, transcription factor (TF) expression and the accessibility of TFs’ cognate motifs. Looking forward, this strategy may facilitate future investigations of gene regulation in vivo at arbitrarily high temporal resolution.
Staged Drosophila embryos were collected in 11 overlapping time windows, collectively spanning 0-20 hrs of development at 25°C. Overlapping two-hour collections were used to capture the rapid transitions during early embryogenesis, followed by overlapping four-hour collections from 4-6 hrs onwards (Fig. 1A). From each such collection, embryo collections were halved and separately processed for single cell ATAC-seq or single cell RNA-seq.