Events Daily

Thursday, November 16, 2023

Noise and Competition: Mechanisms of Gene Expression Control in the Early Embryo
Zeba Wunderlich, Boston University
Event Type: Physics Dept Colloquium
Time: 4:00 PM - 5:30 PM
Location: 726 Broadway, 940, CCPP Seminar
Abstract: Life begins with a single cell that grows and divides and is eventually patterned into diverse cell types. In the early embryo, these cell fate decisions can be rapid, and the gene expression programs that drive these decisions rely on the stochastic interactions of molecules. Nature has evolved many ways to generate reproducible patterns of gene expression in early development despite the inherent noise in the system. In this seminar, I will describe one such mechanism, called shadow enhancers. Enhancers are stretches of regulatory DNA that bind transcription factors to regulate expression of a target gene. Shadow enhancers are seemingly redundant enhancers that control a single target gene and drive overlapping expression patterns. Shadow enhancers control the majority of developmental genes. Using measurements of gene expression dynamics in the Drosophila embryo and mathematical modeling, we probed the mechanism of action for these shadow enhancers. Our results suggest the widespread use of shadow enhancers is partially due to their noise suppressing ability. In related work, we also discovered that a critical tool in studying enhancer dynamics -- reporter constructs -- can perturb the expression of nearby genes by competing for binding transcription factors. To rationalize this unexpected effect -- reporters contain ~10 transcription factor binding sites and cells contain 1000s of copies of transcription factor protein -- we used biophysical estimates of different modes of transcription factor binding. Our measurements and models support the view that transcription factor binding is localized to hubs within the nucleus