Coordinated control of neuronal differentiation and wiring by sustained transcription factors

The large diversity of cell types in nervous systems presents a challenge in identifying the genetic mechanisms that encode it. Here, we report that nearly 200 distinct neurons in the Drosophila visual system can each be defined by unique combinations of on average 10 continuously expressed transcription factors. We show that targeted modifications of this terminal selector code induce predictable conversions of neuronal fates that appear morphologically and transcriptionally complete. Cis-regulatory analysis of open chromatin links one of these genes to an upstream patterning factor that specifies neuronal fates in stem cells. Experimentally validated network models describe the synergistic regulation of downstream effectors by terminal selectors and ecdysone signaling during brain wiring. Our results provide a generalizable framework of how specific fates are implemented in postmitotic neurons.

A complete temporal transcription factor series in the fly visual system

The brain consists of thousands of neuronal types that are generated by stem cells producing different neuronal types as they age. In Drosophila, this temporal patterning is driven by the successive expression of temporal transcription factors (tTFs)^1-6. Here we used single-cell mRNA sequencing to identify the complete series of tTFs that specify most Drosophila optic lobe neurons. We verify that tTFs regulate the progression of the series by activating the next tTF(s) and repressing the previous one(s), and also identify more complex mechanisms of regulation. Moreover, we establish the temporal window of origin and birth order of each neuronal type in the medulla and provide evidence that these tTFs are sufficient to explain the generation of all of the neuronal diversity in this brain region. Finally, we describe the first steps of neuronal differentiation and show that these steps are conserved in humans. We find that terminal differentiation genes, such as neurotransmitter-related genes, are present as transcripts, but not as proteins, in immature larval neurons. This comprehensive analysis of a temporal series of tTFs in the optic lobe offers mechanistic insights into how tTF series are regulated, and how they can lead to the generation of a complete set of neurons.

Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly

For more than 100 years, the fruit fly Drosophila melanogaster has been one of the most studied model organisms. Here, we present a single-cell atlas of the adult fly, Tabula Drosophilae, that includes 580,000 nuclei from 15 individually dissected sexed tissues as well as the entire head and body, annotated to >250 distinct cell types. We provide an in-depth analysis of cell type-related gene signatures and transcription factor markers, as well as sexual dimorphism, across the whole animal. Analysis of common cell types between tissues, such as blood and muscle cells, reveals rare cell types and tissue-specific subtypes. This atlas provides a valuable resource for the Drosophila community and serves as a reference to study genetic perturbations and disease models at single-cell resolution.

Filopodial dynamics and growth cone stabilization in Drosophila visual circuit development

Filopodial dynamics are thought to control growth cone guidance, but the types and roles of growth cone dynamics underlying neural circuit assembly in a living brain are largely unknown. To address this issue, we have developed long-term, continuous, fast and high-resolution imaging of growth cone dynamics from axon growth to synapse formation in cultured Drosophila brains. Using R7 photoreceptor neurons as a model we show that >90% of the growth cone filopodia exhibit fast, stochastic dynamics that persist despite ongoing stepwise layer formation. Correspondingly, R7 growth cones stabilize early and change their final position by passive dislocation. N-Cadherin controls both fast filopodial dynamics and growth cone stabilization. Surprisingly, loss of N-Cadherin causes no primary targeting defects, but destabilizes R7 growth cones to jump between correct and incorrect layers. Hence, growth cone dynamics can influence wiring specificity without a direct role in target recognition and implement simple rules during circuit assembly.

DOI:http://dx.doi.org/10.7554/eLife.10721.001

Genes encode complicated developmental processes, but it is clear that genetic information cannot encode each and every individual connection that forms between the nerve cells in a brain. Instead, the individual cells and nerve endings must make decisions during brain development. Up until now, few examples were known for how these nerve endings move and choose their paths and partners in a living, developing brain.

The fruit fly Drosophila provides a useful model to explore the ‘wiring’ of nerve cells in the brain, partly because a fruit fly’s brain develops within a few days. However, most previous studies have relied on identifying mutant flies with disrupted brain wiring and studying them using still images. Now, Özel et al. have developed a new imaging method that has enough resolution and speed over sufficiently long periods to track the growing nerve endings in a developing fly brain. The method was applied to a model nerve cell in the fly’s visual system. This revealed that most of this nerve’s dynamic changes are short-lived and random, and appear to help to stabilize the developing nerve ending, rather than guide it to a target. Özel et al. also found that a protein called N-Cadherin, previously thought to be required for the targeting of developing nerve endings, actually plays a role in their stabilization.

These findings uncover the roles of changes in nerve endings during long-term brain development; this was previously largely unknown for any organism. The next stage in this research will involve further analyses of both wild type and mutant flies to try and work out general principles about how the brain develops via the decoding of genetic information.

DOI:http://dx.doi.org/10.7554/eLife.10721.002