Dissecting neuron-specific functions of circadian genes using modified cell-specific CRISPR approaches

Circadian behavioral rhythms in Drosophila melanogaster are regulated by about 75 pairs of brain neurons. They all express the core clock genes but have distinct functions and gene expression profiles. To understand the importance of these distinct molecular programs, neuron-specific gene manipulations are essential. Although RNAi based methods are standard to manipulate gene expression in a cell-specific manner, they are often ineffective, especially in assays involving smaller numbers of neurons or weaker Gal4 drivers. We and others recently exploited a neuron-specific CRISPR-based method to mutagenize genes within circadian neurons. Here we further explore this approach to mutagenize three well-studied clock genes: the transcription factor gene vrille, the photoreceptor gene Cryptochrome (cry) and the neuropeptide gene Pdf. The CRISPR-based strategy not only reproduced their known phenotypes but also assigned cry function for different light mediated phenotypes to discrete, different subsets of clock neurons. We further tested two recently published methods for temporal regulation in adult neurons, inducible Cas9 and auxin-inducible gene expression system (AGES). The results were not identical, but both approaches successfully showed that the adult-specific knockout of the neuropeptide Pdf reproduces the canonical loss-of-function mutant phenotypes. In summary, a CRISPR-based strategy is a highly effective, reliable, and general method to temporally manipulate gene function in specific adult neurons. Significance statementMost animals have specific brain neurons that regulate sleep-wake cycles and other aspects of circadian behavior. Drosophila has only about 150 of these clock neurons. Despite their small numbers, they have remarkably diverse anatomy and gene expression profiles. To address the different functions of these neurons, we used highly specific and efficient CRISPR-based methods to create cell type-specific disruptions of three traditional circadian genes. We were able to assign the function of the photoreceptor cryptochrome to two tiny subsets of clock neurons. In addition, two independent methods assigned the neuropeptide PDF to the adult stage. In summary, we find that the CRISPR-based methods are very efficient at studying adult specific functions of genes in small, discrete sets of neurons.