Using single-cell RNA sequencing to generate predictive cell-type-specific genetic drivers

What is it about?

In Drosophila the availability of cell-type specific so-called drivers for selectively expressing genes of interest in a cell type specific way has revolutionized the study of circuit function and behavior. These reagents largely come from a comprehensive screen of small fragments of DNA taken from genes expressed in neurons. These typically give rise to expression domains encompassing many cell types. By intersecting two lines and utilizing the split transcriptional DNA binding and transcription activation domains of GAL4 expressed in each of these lines allows for often highly specific expression in specific cell types. These so-called Split-GAL4 lines have been important in providing highly cell type specific reagents for manipulating adult neural circuitry. In principle, a similar approach could be taken for studying development. Regrettably, the adult expression patterns driven by specific DNA fragments can be quite different than patterns during development. Here we describe a clever and powerful way to reliably develop cell-type specific drivers for developmental studies We leverage the extensive single cell sequencing data available for the developing fly visual system to identify specific genes and combination of genes expressed only in specific cell types. We show that computationally mining these data one can identify specific genes and combinations of two of them selective for a single cell type at multiple developmental stages for the majority of cell types in the visual system. We demonstrate that these can drive cell-type-specific expression patterns during development as predicted in populations of specific neuron types.

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Photo by Chris Curry on Unsplash

Photo by Chris Curry on Unsplash

Why is it important?

These reagents and the approach pioneered here provide extraordinary reagents for the field to ask developmental questions in a particularly precise way. Although we have focused on the fly visual system it is clear that this approach can be used in any region of Drosophila where single cell developmental transcriptomic analysis is available.

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