Genes are transcribed into mRNA before they can be translated into proteins. Thus, transcriptional control is the primary mechanism that determines the flow of genetic information. Which genes are active is determined by genetic control regions, such as enhancers, that are associated with each gene. In a complex dance, transcriptional regulatory proteins bind these control regions to modulate the rate of gene transcription.   

Regulatory genes control expression of other regulatory genes and link together to form gene regulatory networks. While much has been learned about the regulatory logic that underlies basic embryonic patterning, many questions remain regarding how a few regulatory proteins control a precise program of hundreds, sometimes thousands, of genes to propel embryonic development.  

A vast majority of nucleotide variants associated with human diseases are located in non-coding DNA regions where they are thought to affect gene expression. Although for some genes the molecular mechanisms of gene regulation are well understood, for most genes they remain elusive. As a result, predicting the effects of regulatory variants is extremely difficult; instead, these variants must be tested experimentally. 

Here is a list of approaches that we are either developing or applying to questions in early development. Our model system is the zebrafish embryo, where we focus on specification of endoderm and mesodermal cell types, such as vascular progenitors and dorsal forerunner cells.

  • Parallel reporter assays to query enhancer activity.
  • Protein tagging for visualization of endogenous proteins using split-fluorescent proteins (in collaboration with our friends in the Woo lab).
  • Transcriptional profiling of early zebrafish embryos by single cell sequencing and RNA tagging.
  • Molecular characterization of transcription factor function.