In the Drosophila optic lobes, the medulla processes visual information coming from inner photoreceptors R7 and R8 and from lamina neurons. It contains approximately 40,000 neurons belonging to more than 70 different types. Here we describe how precise temporal patterning of neural progenitors generates these different neural types. Five transcription factors—Homothorax, Eyeless, Sloppy paired, Dichaete and Tailless—are sequentially expressed in a temporal cascade in each of the medulla neuroblasts as they age. Loss of Eyeless, Sloppy paired or Dichaete blocks further progression of the temporal sequence. We provide evidence that this temporal sequence in neuroblasts, together with Notch-dependent binary fate choice, controls the diversification of the neuronal progeny. Although a temporal sequence of transcription factors had been identified in Drosophila embryonic neuroblasts, our work illustrates the generality of this strategy, with different sequences of transcription factors being used in different contexts.

The Drosophila eye is a mosaic that results from the stochastic distribution of two ommatidial subtypes. Pale and yellow ommatidia can be distinguished by the expression of distinct rhodopsins and other pigments in their inner photoreceptors (R7 and R8), which are implicated in color vision. The pale subtype contains ultraviolet (UV)-absorbing Rh3 in R7 and blue-absorbing Rh5 in R8. The yellow subtype contains UV-absorbing Rh4 in R7 and green-absorbing Rh6 in R8. The exclusive expression of one rhodopsin per photoreceptor is a widespread phenomenon, although exceptions exist. The mechanisms leading to the exclusive expression or to co-expression of sensory receptors are currently not known. We describe a new class of ommatidia that co-express rh3 and rh4 in R7, but maintain normal exclusion between rh5 and rh6 in R8. These ommatidia, which are localized in the dorsal eye, result from the expansion of rh3 into the yellow-R7 subtype. Genes from the Iroquois Complex (Iro-C) are necessary and sufficient to induce co-expression in yR7. Iro-C genes allow photoreceptors to break the “one receptor–one neuron” rule, leading to a novel subtype of broad-spectrum UV- and green-sensitive ommatidia. Most sensory systems follow the rule “one receptor molecule per receptor cell.” For example, photoreceptors in the fly eye and cones in the human eye each express only one light-sensitive rhodopsin. Rhodopsins are G-coupled protein receptors, a class of ancient signaling molecules that mediate not just vision but also the sense of smell, the inflammatory response, and other physiological processes. However, the mechanisms that regulate mutual exclusion of receptor genes in the visual and olfactory systems are poorly understood. Each ommatidium in the fly eye consists of eight photoreceptors (R1–R8); six of which mediate broad-spectrum motion vision (R1–R6) and two that mediate color vision (R7 and R8). We identified a new class of photoreceptors in the fly retina that violates the one rhodopsin–one receptor rule. This subset of ommatidia, located in the dorsal third of the eye, co-expresses two ultraviolet-sensitive rhodospins (rh3 and rh4) in R7, while maintaining discrimination between green and blue opsins in R8. We took advantage of the genetic tools offered by the fruit fly to show that this co-expression depends on the Iroquois Complex (Iro-C) genes that are both necessary and sufficient to allow the two ultraviolet-sensitive rhosopsins to be expressed in the same R7 cell. These results shed new light on the mechanisms regulating co-expression of rhodopsins in the eye, and may well have implications for regulating co-expression in olfactory receptors and other G-protein coupled systems.

Genome control is operated by transcription factors (TFs) controlling their target genes by binding to promoters and enhancers. Conceptually, the interactions between TFs, their binding sites, and their functional targets are represented by gene regulatory networks (GRNs). Deciphering in vivo GRNs underlying organ development in an unbiased genome-wide setting involves identifying both functional TF-gene interactions and physical TF-DNA interactions. To reverse engineer the GRNs of eye development in Drosophila, we performed RNA-seq across 72 genetic perturbations and sorted cell types and inferred a coexpression network. Next, we derived direct TF-DNA interactions using computational motif inference, ultimately connecting 241 TFs to 5,632 direct target genes through 24,926 enhancers. Using this network, we found network motifs, cis-regulatory codes, and regulators of eye development. We validate the predicted target regions of Grainyhead by ChIP-seq and identify this factor as a general cofactor in the eye network, being bound to thousands of nucleosome-free regions.

Some of the senses, such as colour vision and olfaction, rely on single sensory neurons to produce a specific chemical- or light-sensing G-protein coupled receptor. Various mechanisms have been proposed to explain exclusive gene expression in olfactory receptors, but the molecular pathways remain unknown. Claude Desplan and colleagues report that mature Drosophila R8 photoreceptors of the subtype that normally expresses green-sensing rhodopsin 6 protein can express the 'wrong' blue-sensing rhodopsin 5 when fruitflies are either kept in the dark or mutated in rhodopsin 6. Light thus achieves a negative feedback on the rh5 gene by repressing its transcription in rh6-expressing neurons, a system resembling the control of olfactory receptor genes in vertebrate olfactory neurons. Sensory systems with high discriminatory power use neurons that express only one of several alternative sensory receptor proteins. This exclusive receptor gene expression restricts the sensitivity spectrum of neurons and is coordinated with the choice of their synaptic targets1,2,3. However, little is known about how it is maintained throughout the life of a neuron. Here we show that the green-light sensing receptor rhodopsin 6 (Rh6) acts to exclude an alternative blue-sensitive rhodopsin 5 (Rh5) from a subset of Drosophila R8 photoreceptor neurons4. Loss of Rh6 leads to a gradual expansion of Rh5 expression into all R8 photoreceptors of the ageing adult retina. The Rh6 feedback signal results in repression of the rh5 promoter and can be mimicked by other Drosophila rhodopsins; it is partly dependent on activation of rhodopsin by light, and relies on Gαq activity, but not on the subsequent steps of the phototransduction cascade5. Our observations reveal a thus far unappreciated spectral plasticity of R8 photoreceptors, and identify rhodopsin feedback as an exclusion mechanism.