No abstract

Transcription factors (TFs) regulate transcription of their target genes by identifying and binding to regulatory regions of the genome among billions of potential non-specific decoy sites, a task that is often presented as a ‘needle in the haystack’ challenge. The TF search process is now well understood in bacteria, but its characterization in eukaryotes needs to account for the complex organization of the nuclear environment. Here we review how live-cell single molecule tracking is starting to shed light on the TF search mechanism in the eukaryotic cell and we outline the future challenges to tackle in order to understand how nuclear organization modulates the TF search process in physiological and pathological conditions.

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.