Abstract
Precise patterns of synaptic connections between neurons are encoded in their genetic programs. Here, we use single-cell RNA sequencing to profile neuronal transcriptomes at multiple stages in the developing Drosophila visual system. We devise an efficient strategy for profiling neurons at multiple time points in a single pool, thereby minimizing batch effects and maximizing the reliability of time-course data. A transcriptional atlas spanning multiple stages is generated, including more than 150 distinct neuronal populations; of these, 88 are followed through synaptogenesis. This analysis reveals a common (pan-neuronal) program unfolding in highly coordinated fashion in all neurons, including genes encoding proteins comprising the core synaptic machinery and membrane excitability. This program is overlaid by cell-type-specific programs with diverse cell recognition molecules expressed in different combinations and at different times. We propose that a pan-neuronal program endows neurons with the competence to form synapses and that cell-type-specific programs control synaptic specificity.
•Multiplex single-cell sequencing of many developing brain samples in parallel•mRNA expression of >150 Drosophila visual system neurons throughout development•A synchronous pan-neuronal program regulates gene expression in different neurons•Dynamic cell-type-specific expression of cell surface proteins during wiring
Kurmangaliyev et al. use a genetic multiplexing strategy to generate a comprehensive atlas of the developing Drosophila visual system. This atlas includes transcriptional programs for more than 150 distinct neuronal populations. It covers multiple stages of neuronal development, from the early steps of circuit assembly to the adult functional brain.