NIH’s 4D Nucleome program issued a new set of studies describing how chromatin structure and DNA methylation shape gene regulation across tissues and disease states. The updated wave of publications—spanning Science and Science Advances—uses single-cell multi-omics to connect epigenetic layers and cellular phenotypes in health and pathology. The program’s new work includes analyses of spatial reorganization and regulatory dynamics relevant to heart disease, Alzheimer’s disease, brain aging, retinal health, and immune cell development. The emphasis is on tracking noncoding genome features and linking architectural changes to gene expression programs in individual cells. In parallel, earlier 4D Nucleome papers have focused on simultaneous profiling of 3D genome organization and DNA methylation, creating direct comparisons of how each epigenetic layer reflects cell identity and disease risk. For drug developers and translational researchers, the growing single-cell atlases and analytical tooling from 4D Nucleome expand the toolkit for identifying regulatory mechanisms that may drive target selection and biomarkers.