Much of the diversity within and between animal species arises due to sequence differences in the vast noncoding regions of the genome. These regions are not transcribed to produce proteins, but rather interact with one another to regulate just which proteins a cell expresses and how much of each it uses. The biophysical mechanisms underlying these interactions are poorly understood, though much evidence indicates the local 3D folding of the genome inside the nucleus plays an instrumental role. My lab seeks to understand how interactions among noncoding sequences regulate gene expression by developing new microscopy approaches to simultaneously observe transcription, protein binding, and the 3D nanostructure of the genome around key developmental genes in individual nuclei of animal embryos with detail and resolution never before achieved. We combine our microscopy with advanced genetic editing of noncoding sequences to understand how they affect 3D folding and gene expression.