GSE163307
Drosophila L3 ATAC-seq at 24h APF
The layered compartmentalization of functionally-related synaptic connections, a common feature of nervous systems, underlies proper connectivity between neurons and enables parallel processing of neural information. However, the stepwise development of layered neuronal connections is not well understood. The medulla neuropil of the Drosophila melanogaster visual system is comprised of 10 discrete layers (M1-M10), within which neural computations underlying distinct visual features are processed. As such, the Drosophila medulla neuropil serves as a model system for understanding layered compartmentalization of synaptic connectivity. The first step leading to the establishment of neurite layer specificity in the outer medulla (M1-M6) is the innervation of one of two broad, primordial domains that will subsequently expand and transform into the M1-M6 layers. We previously found that the transcription factor dFezf cell-autonomously directs L3 neurons to their proper early broad domain before they innervate and form synapses specifically within the M3 layer of the mature medulla. Here, we examined the transcriptomes of wild type and dFezf mutant L3 neurons by RNA-seq and identified downstream target genes that are regulated by dFezf. We show that dFezf controls L3 layer specificity through temporally precise transcriptional repression of the transcription factor slp1 (sloppy paired 1). During the period of broad domain selection, dFezf limits slp1 expression in L3 neurons. Slp1 is upregulated in dFezf-null L3 neurons, and ablation of slp1 fully rescues the targeting defect observed in dFezf-null L3 growth cones. Surprisingly, L3 innervation of the M3 layer after broad domain selection requires early slp1 expression. DFezf thus functions as a transcriptional repressor to coordinate the temporal dynamics of a transcriptional cascade that orchestrates sequential steps of layer-specific synapse formation. Moreover, we performed ATAC-seq in wild type L3 neurons and identified the accessible regions in the L3 genome, where dFezf may directly bind and regulate gene expression. Overall design: Fluorescently-labeled wild type L3 neurons were isolated by FACS at 24h APF. DNA libraries were made from genomic DNA and sequenced using an Illumina platform. Three biological replicates were performed. All three libraries were prepared and sequenced at the same time to minimize technical variability.