3/20 - Seminar (chem bio): James Chen, Stanford University
James Chen - speaker's webpage
School of Medicine
Host: Tom Muir
Chemical probes of embryonic signaling and patterning
Embryonic development is controlled by an ensemble of signaling pathways that are dynamically activated in space and time. Dramatic morphological changes can occur within minutes and with single-cell resolution, and the chemical reactions and interactions that underlie these processes take place on even more exacting scales. Elucidating the molecular mechanisms of pattern formation therefore requires experimental techniques that can modulate these pathways with comparable facility. While genetic technologies have traditionally been used to achieve these perturbations, chemical probes are valuable additions to developmental biologist’s toolbox. Here I describe two examples of how chemical tools can be used to interrogate embryonic signaling and patterning. First, by conducting a high-throughput screen for Hedgehog pathway inhibitors, we have discovered a family of small molecules that block Gli transcription factor function and primary cilia formation. Through cell-based and in vitro studies, we have established these compounds as the first specific inhibitors of cytoplasmic dynein, which is required for retrograde ciliary trafficking and therefore Gli regulation. Second, we show how temporal, tissue-specific changes in transcription factor function can be discerned by integrating caged antisense oligonucleotides, photoactivatable fluorophores, fluorescence-activated cell sorting, and transcriptome analysis. As a proof of principle, we have dynamically profiled No tail-a (Ntla)/Brachyury-dependent genes at different stages of axial mesoderm development in zebrafish. These studies have identified discrete sets of Ntla-dependent transcripts that are coincident with notochord cell fate commitment or differentiation, revealing a surprising degree of transcription factor plasticity within a single cell lineage.