Curated Optogenetic Publication Database

Abstract: System identification approaches are commonly used in engineering to infer simple yet predictive models of complex systems from their responses to time-dependent perturbations. Here, we apply this strategy at the whole organism scale, establishing a predictive model of commitment to metamorphosis in Drosophila. At this critical point in animal development, the larva stops feeding and proceeds to take on the adult form. The neuroendocrine circuits governing commitment to metamorphosis assess the growth and patterning programs, eventually triggering the production of systemic hormones that terminate growth and initiate metamorphosis. Previous studies of these circuits relied on relatively static genetic perturbations and starvation experiments. Here, we take advantage of optogenetic approaches in Drosophila to flexibly perturb a key signaling node within the endocrine gland in otherwise undisturbed larvae. We used this approach to infer parameters in a compact mathematical model and demonstrate that it makes accurate predictions of larval commitment to metamorphosis. Our work paves the way for quantitative studies of other juvenile-to-adult transitions, including mammalian puberty, which relies on strikingly similar mechanisms.

Abstract: Extracellular-signal-regulated kinase (ERK) signaling controls development and homeostasis and is genetically deregulated in human diseases, including neurocognitive disorders and cancers. Although the list of ERK functions is vast and steadily growing, the full spectrum of processes controlled by any specific ERK activation event remains unknown. Here, we show how ERK functions can be systematically identified using targeted perturbations and global readouts of ERK activation. Our experimental model is the Drosophila embryo, where ERK signaling at the embryonic poles has thus far only been associated with the transcriptional patterning of the future larva. Through a combination of live imaging and phosphoproteomics, we demonstrated that ERK activation at the poles is also critical for maintaining the speed and synchrony of embryonic cleavages. The presented approach to interrogating phosphorylation networks identifies a hidden function of a well-studied signaling event and sets the stage for similar studies in other organisms.

Abstract: Optogenetic perturbations, live imaging, and time-resolved ChIP-seq assays in Drosophila embryos were used to dissect the ERK-dependent control of the HMG-box repressor Capicua (Cic), which plays critical roles in development and is deregulated in human spinocerebellar ataxia and cancers. We established that Cic target genes are activated before significant downregulation of nuclear localization of Cic and demonstrated that their activation is preceded by fast dissociation of Cic from the regulatory DNA. We discovered that both Cic-DNA binding and repression are rapidly reinstated in the absence of ERK activation, revealing that inductive signaling must be sufficiently sustained to ensure robust transcriptional response. Our work provides a quantitative framework for the mechanistic analysis of dynamics and control of transcriptional repression in development.