Transcriptional activators in the early Drosophila embryo perform different kinetic roles

• Published in: Cell systems Vol. 14; no. 4; pp. 258 - 272.e4
• Main Authors: Harden, Timothy T., Vincent, Ben J., DePace, Angela H.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 19.04.2023
• Subjects: Animals; D. melanogaster embryo; diSPIM; Drosophila melanogaster - embryology; Drosophila melanogaster - metabolism; Drosophila Proteins - genetics; Drosophila Proteins - metabolism; Gene Expression Regulation, Developmental; kinetic modeling; Kinetics; MS2/MCP live imaging; Promoter Regions, Genetic; transcription factors; Transcription Factors - genetics; Transcription Factors - metabolism; transcription regulation; Transcription, Genetic; D. melanogaster embryo; transcription regulation; MS2/MCP live imaging; transcription factors; diSPIM; kinetic modeling
• ISSN: 2405-4712; 2405-4720
• DOI: 10.1016/j.cels.2023.03.006

Combinatorial regulation of gene expression by transcription factors (TFs) may in part arise from kinetic synergy—wherein TFs regulate different steps in the transcription cycle. Kinetic synergy requires that TFs play distinguishable kinetic roles. Here, we used live imaging to determine the kinetic roles of three TFs that activate transcription in the Drosophila embryo—Zelda, Bicoid, and Stat92E—by introducing their binding sites into the even-skipped stripe 2 enhancer. These TFs influence different sets of kinetic parameters, and their influence can change over time. All three TFs increased the fraction of transcriptionally active nuclei; Zelda also shortened the first-passage time into transcription and regulated the interval between transcription events. Stat92E also increased the lifetimes of active transcription. Different TFs can therefore play distinct kinetic roles in activating the transcription. This has consequences for understanding the composition and flexibility of regulatory DNA sequences and the biochemical function of TFs. A record of this paper’s transparent peer review process is included in the supplemental information. [Display omitted] •TFs can perform distinguishable kinetic roles when activating the transcription•Individual TFs can perform multiple kinetic roles, some of which overlap with other TFs•We use a simple method to infer kinetic roles using live imaging•We used coarse-grained, empirical math models to compare kinetic roles We demonstrate that in animals, the proteins that control gene expression can activate a gene in different ways. Our results support a mechanism called kinetic synergy, where proteins with distinct dynamic roles collaborate to turn on a gene.