Cell-type-specific circadian and light-responsive transcriptional dynamics in adult Drosophila neurons

Recent single cell RNA-seq (scRNAseq) characterization of these neurons “around the clock” also indicate a similar number of circadian neuron subtypes, but other conclusions from these transcriptomic studies warranted verifying and extending with other approaches. To this end: 1) We used the Drosophila Genetic Reference Panel (DGRP) multiplexing strategy to eliminate 10X batch effects and profile time points together; 2) Large numbers of single nuclei were sequenced (snRNA-seq), which was enabled because the new method EL-INTACT purifies nuclei from frozen heads; 3) We assayed 12 time points under both light–dark (LD) and constant darkness (DD) conditions.

These approaches showed dramatic time of day separation of many circadian neuron types and enhanced time-of-day gene expression analysis. The data indicate that most of this regulation is transcriptional and circadian. There were however a small number of light-dependent transcripts, including a few that correspond to mammalian immediate-early genes.