The Murphy lab investigates the mechanisms that activate or silence genes as cells transition from one state to another. In very early embryos, stem cells begin to divide and change. Through this process, called differentiation, tissues begin to form, and all the cell types of the organism start to arise. Differentiation depends on a highly coordinated series of gene activation and silencing events. As cells divide during this process, changes in gene expression give each cell type its specific identity and function. Similarly, when gene expression patterns in normal adult cells change inappropriately, cell identity can shift—potentially leading to carcinogenesis. However, the molecular machinery that enables a cell to transition from one gene expression state to another remains unknown.

Understanding how cells transition between states is a central question in the biological sciences, with particular significance for studies of organismal development, reproduction, carcinogenesis, and pluripotent reprogramming. In the early days of developmental biology (1940s–50s), Conrad Waddington coined the term epigenetics to describe the process by which a cell transitions from one state to another during development. He also used the term to explore how gene–environment interactions influence cell fate. Since Waddington’s early work, the definition of epigenetics has evolved many times and now broadly encompasses the molecular mechanisms that regulate gene activation and silencing, among other functions.

In the Murphy lab, we use zebrafish and mouse model organisms to investigate how epigenetic marks control gene expression patterns and drive cell state transitions. We focus on gametogenesis, stem cell formation, and the initial phases of differentiation in embryos. Our research combines classical genetics and developmental biology with modern DNA sequencing technologies and bioinformatics tools to map the genomic locations of various proteins and epigenetic marks as they change during these transitions.