ISWI is an Intrinsically Dynamic Nucleosome Remodeler That Induces Large-scale Histone Dynamics

The chromatin remodeler ISWI plays a crucial role in the maintenance of the dynamic chromatin landscape through its ability to alter nucleosome spacing. Nucleosome remodeling by ISWI involves the translocation of DNA over the histone octamer surface, without disassembly of the nucleosome. Despite the enormous progress in the structural characterization of this process in recent years, it remains unclear to what extent conformational changes in the histone proteins play a role in remodeling. In addition, the conformation and dynamics of regulatory NTR and NegC domains within the remodeler have proven difficult to obtain. Here, we studied the conformational dynamics of fruit fly ISWI and the nucleosome-ISWI complex using solution NMR spectroscopy. We find that the NTR contains a highly dynamic DNA-binding loop and that the NegC domain is packed against ATPase lobe 2 in the free enzyme. Methyl-TROSY data indicate that the ATPase lobes and the NegC domain have substantial μs-ms motions in the free enzyme suggesting that conformational changes during the catalytic cycle are intrinsically encoded. Comparison of histone methyl-TROSY spectra upon binding of different ISWI constructs indicates that binding of a de-inhibited ISWI construct induces largest conformational changes through the histone octamer, affecting histone-DNA and histone-histone contacts. Overall, these findings refine our understanding of the conformational landscape of ISWI and provide strong support for histone plasticity during remodeling to facilitate DNA translocation, highlighting the histone octamer as an allosteric unit.