Many nuclear proteins form dynamic regions of high local concentration, often described as clusters, hubs, or condensates. These structures have been proposed to enhance or organize gene regulation, yet the molecular mechanisms that generate them and their functional consequences remain debated. I will present work combining high-resolution light-sheet microscopy, single-molecule tracking, genomics, and kinetic simulations in live preimplantation mouse embryos and blastoderm-stage Drosophila embryos. Across transcription factors, repressive complexes, and the transcriptional machinery, these approaches reveal how molecular diffusion, chromatin binding, and the distribution of binding sites together shape nuclear protein clustering during development. I will discuss how enhancer sequence encodes the enrichment and persistence of transcription factor clusters, how intrinsically disordered regions tune chromatin search, and how the accumulation of transcriptionally engaged polymerases leads to the appearance of stable clusters at active genes. Together, these results support a framework in which the clustering of nuclear regulatory proteins emerges directly from their molecular kinetics and interactions with the genome.”
