Hard-wired: The transcriptional programs that control wiring diversity in the fly visual system

For normal brain function, an enormous number of neurons must be precisely connected with their correct target neurons. These connections are assembled into neural circuits which process diverse sensory stimuli, control movement, allow the formation and recall of memories, and much more. In Chapter 5 of Principles of Neurobiology, we learned how the visual system uses both “nature” and “nurture” to ensure that retinal ganglion cells find their correct targets in the brain. In the context of “nature”, cell surface molecules can mediate both attractive and repulsive forces guiding axons to their correct targets. What are the transcriptional programs that control cell surface molecule expression? Do different types of neurons have different transcriptional programs? Do transcriptional programs change over the development of a single neuron type?

In the last few years, advances in single-cell RNA-sequencing (scRNA-seq) have allowed the transcriptomic profile of different neuron types at different stages of development to be compared. This has provided great insight into the types of genes that are expressed at certain points in development and how transcriptomic profiles compare between cells with similar or different patterns of connectivity. Recently, Kurmangaliyev et al. and Özel et al. published two independent studies that performed scRNA-seq to generate transcriptomic atlases of the Drosophila visual system across multiple developmental stages (Figure A). Both studies isolated single cells from optic lobes at early-pupal, mid-pupal, late-pupal and adult stages.

Connectivity patterns of different neuron types are distinct and therefore each neuron type must contain unique transcriptomes that underlie the cell type-specific wiring patterns. Kurmangaliyev et al. focused on eight cell types that have different connectivity patterns. Among these 8 cell types, 362 genes were labeled as highly variable. Transcription factors and cell-surface molecules were key contributors to neuronal transcriptome diversity – in these 8 types 41% of highly variable genes were transcription factors or cell surface molecules. Different gene types had variable expression signatures over development. Transcription factors tended to exhibit binary expression amongst cell types and were expressed at all stages of development. In contrast, cell adhesion molecules were more transiently expressed during development and the same cell adhesion molecule could switch expression between different cell types and different timepoints. Genes related to post-transcriptional and post-translational mechanisms also had neuron type specific expression and could contribute to neuron diversity by mediating alternative splicing of uniformly expressed cell surface molecules.

Both groups found that different neuron types are more easily distinguished in mid-pupal stages rather than early development or adult. Özel et al. investigated the transcriptome signatures that underlie this feature. They looked at what gene types were prominent in each neuronal subtype at each stage of development (Figure B). At all stages of development there was significant enrichment of genes known to be involved in axon/dendrite development and synapse formation, then transcription factors and ion channels. To determine what caused the increased diversity they observed in mid-pupal stages they look at genes that were upregulated in neurons at a particular stage compared to other developmental stages. They found that cell surface molecules involved in synapse formation and membrane potential regulation were significantly upregulated and the cause of the increased diversity at these mid-pupal stages. Early pupal stages had increased expression of genes related to protein synthesis and in adult stages the genes were related to energy metabolism. This suggested that the increased expression of cell surface molecules in mid-pupal stages to allow precise connectivity and synaptic specificity are the reason for the greatest transcriptional diversity at these stages. This diversity is lost as neurons mature, particularly between neuron sub-types that perform similar functions but have different connectivity. Once the different connectivity is established during development, there is no need for these molecules to still be expressed. A previous study on neurons of the developing fly olfactory system made similar findings.

These atlases now allow researchers to identify genes of interest and test their roles in precise wiring of different cell types in the visual system. The same strategy is being applied to many other networks within the central nervous system of different species and will ultimately provide key insights into the types of genes required at different stages for the formation of neuron specific connectivity patterns.

Figure adapted from Kurmangaliyev et al. (2020) (A) and Özel et al. (2021) (B)

A) Distinct transcriptional clusters of different neuron types from Kurmangaliyev et al. (2020). 162 transcriptionally distinct neuronal populations were identified across development.
B) Summary of enriched genes and their related molecular functions at different stages across development.

Reference

Kurmangaliyev, Y.Z., Yoo, J., Valdes-Aleman, J., Sanfilippo, P., and Zipursky, S.L. (2020). Transcriptional Programs of Circuit Assembly in the Drosophila Visual System. Neuron 108, 1045-1057.e6. Link

Özel, M.N., Simon, F., Jafari, S., Holguera, I., Chen, Y.-C., Benhra, N., El-Danaf, R.N., Kapuralin, K., Malin, J.A., Konstantinides, N., et al. (2021). Neuronal diversity and convergence in a visual system developmental atlas. Nature 589, 88–95. Link