Optogenetic control of the Bicoid morphogen reveals fast and slow modes of gap gene regulation

• Published in: Cell reports (Cambridge) Vol. 38; no. 12; p. 110543
• Main Authors: Singh, Anand P., Wu, Ping, Ryabichko, Sergey, Raimundo, João, Swan, Michael, Wieschaus, Eric, Gregor, Thomas, Toettcher, Jared E.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 22.03.2022; Elsevier
• Subjects: Animal genetics; Bicoid; Biochemistry, Molecular Biology; Biophysics; CP: Cell Biology; Development Biology; Drosophila development; Drosophila Proteins; Drosophila Proteins - metabolism; gap gene network; Gene Expression Regulation, Developmental; Genetics; Homeodomain Proteins; Homeodomain Proteins - metabolism; kinetics; Life Sciences; live imaging; Optogenetics; Trans-Activators; Trans-Activators - metabolism; transcription; live imaging; transcription; Drosophila development; optogenetics; Bicoid; gap gene network; kinetics; CP: Cell Biology
• ISSN: 2211-1247; 2211-1247
• DOI: 10.1016/j.celrep.2022.110543

Developmental patterning networks are regulated by multiple inputs and feedback connections that rapidly reshape gene expression, limiting the information that can be gained solely from slow genetic perturbations. Here we show that fast optogenetic stimuli, real-time transcriptional reporters, and a simplified genetic background can be combined to reveal the kinetics of gene expression downstream of a developmental transcription factor in vivo. We engineer light-controlled versions of the Bicoid transcription factor and study their effects on downstream gap genes in embryos. Our results recapitulate known relationships, including rapid Bicoid-dependent transcription of giant and hunchback and delayed repression of Krüppel. In addition, we find that the posterior pattern of knirps exhibits a quick but inverted response to Bicoid perturbation, suggesting a noncanonical role for Bicoid in directly suppressing knirps transcription. Acute modulation of transcription factor concentration while recording output gene activity represents a powerful approach for studying developmental gene networks in vivo. [Display omitted] •Rapid optogenetic Bcd control is combined with measurement of target gene dynamics•hb and gt transcription responds in around 5 min to changes in nuclear Bcd•Acute changes in Bcd concentration drive delayed repression of Kr•kni transcription is initiated rapidly upon depletion of nuclear Bcd Singh et al. investigate how rapid changes in nuclear Bicoid levels dynamically regulate expression of its target genes. Combining optogenetic stimulation and a simplified genetic background, their results recapitulate the canonical role of Bicoid as a transcriptional activator and reveal a possible noncanonical role in direct kni repression.