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.

Featured Image

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.


In this work, we developed two useful websites for all fly researchers: 1) single-cell Marker Combination finder (scMarco), a Graphical User Interface, designed to find marker gene pairs. You can explore the gene expression in any clusters in the optic lobes across development. Here is the link: https://apps.ycdavidchen.com/scMarco For researchers working on different tissues, you can create this Shiny web application using your own single-cell RNA sequencing data and have an easy exploration of your own dataset. The documentation described the steps to do that is linked here: https://docs.ycdavidchen.com/scMarco 2) splitgal4.org: This is a centralized database for the gene-specific split-GAL4 lines generated by this study (~100 split-GAL4 lines!) and others in the fly community. The beauty of these gene-specific split-GAL4 lines is that everyone working on different fly tissues can use them! I am constantly making more gene-specific split-GAL4 lines by crosses. Feel free to contact me if you have any questions!

Yu-Chieh David Chen
New York University

Read the Original

This page is a summary of: Using single-cell RNA sequencing to generate predictive cell-type-specific split-GAL4 reagents throughout development, Proceedings of the National Academy of Sciences, July 2023, Proceedings of the National Academy of Sciences, DOI: 10.1073/pnas.2307451120.
You can read the full text:




The following have contributed to this page