Chromatin organization drives the exploration strategy of nuclear factors

Nuclear Factors (NFs) rapidly scan the genome for their targets, but the role of nuclear organization in such search is unexplored. To address this, we combined live-cell single-molecule tracking of NFs with multifocal structured illumination of DNA density and characterized the exploration strategy of multiple NFs, including the tumor suppressor p53. p53 alternates between rapid diffusion in the interchromatin compartment (IC) and compact sampling of chromatin dense regions (CDs). This slowed down diffusion – mediated by p53 intrinsically disordered regions (IDRs) – directs p53 to its binding sites in CDs surrounded by IC channels. Efficient targeting requires balanced IDR/chromatin interactions: strong IDRs potentiate target gene activation, but excessive IDR/IDR interactions lead to p53 condensates, derailing its search and downregulating transcription. Our findings highlight the role of NF IDRs on their search and showcase a powerful method to generate traffic maps of the eukaryotic nucleus and dissect how nuclear organization guides NFs action.