Chromatin remodeling in condensed and phase separated chromatin
Petra Vizjak1,2, Dieter Kamp2, Johannes Stiegler2, Felix Müller-Planitz1
1TU Dresden, Dresden, Germany,
2LMU, Munich, Germany
Chromatin compacts and regulates the genomes of eukaryotes. Recently, it was discovered that chromatin can undergo phase separation. Phase separation provides profound challenges for cellular factors. (How) can chromatin factors enter these dense condensates, can they work in such a crowded environment, and how can they diffuse efficiently through the condensate? In fact, highly condensed chromatin has previously often been considered to be largely inaccessible to cellular factors.
We challenge this view at the example of the chromatin remodeling enzyme ISWI. Drawing energy from ATP hydrolysis, it slides nucleosomes along DNA. We show that neither chromatin folding nor condensation impedes nucleosome sliding in vitro. To this end, we developed an imaging-based nucleosome sliding assay, which allowed us to compare remodeling rates in- and outside of chromatin condensates. Using optical tweezers, we documented that ISWI hardens chromatin condensates whenever ATP hydrolysis is not permitted. Active hydrolysis is also required for ISWI’s mobility inside condensates. ATP hydrolysis has therefore a dual use: it is not only needed for nucleosome sliding but also for propelling ISWI through dense condensates.
We propose a ‘monkey-bar’ model, in which ISWI can grab a neighboring nucleosome, or withdraw from it, in an ATP hydrolysis dependent manner. Molecular dynamics simulations of the model broadly agree with our data. We speculate that such ‘monkey-bar’ mechanisms could be shared more broadly by other chromatin factors. Our findings further suggest that pathologies induced by corrupted chromatin remodelers might be caused in part by changes in chromatin dynamics, and not exclusively by disruption of canonical remodeler functions.