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Chromatin organization drives the exploration strategy of nuclear factors

Mazzocca, M.; Loffreda, A.; Colombo, E.; Fillot, T.; Gnani, D.; Falletta, P.; Monteleone, E.; Capozi, S.; Bertrand, E.; Legube, G.; Lavagnino, Z.; Tacchetti, C.; Mazza, D.

2022-12-29 biophysics
10.1101/2022.12.29.522193 bioRxiv
Show abstract

Nuclear Factors (NFs) rapidly scan the genome for their targets, but the role of nuclear organization in such search is uncharted. Here we analyzed how multiple NFs explore chromatin, by combining live-cell single-molecule tracking with multifocal structured illumination of DNA density. We find that NFs displaying higher bound fractions sample DNA dense regions more exhaustively. Focusing on the tumor-suppressor p53, we demonstrated that this NF search for its targets by alternating between rapid diffusion in the interchromatin compartment and compact sampling of chromatin dense regions. Efficient p53 targeting requires balanced IDR/chromatin interactions: adding an exogenous IDR potentiates p53-mediated 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.

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