Any biological process involving the genome – be it transcription, replication or repair – requires the remodelling of histone-DNA interactions. This remodelling is achieved by ATP-dependent DNA translocase enzymes. We set out to determine the mechanism by which one prominent remodeller – the CHD4 – can move histones relative to DNA. We have used both bulk and single-molecule FRET measurements to demonstrate that the binding energy for CHD4-nucleosome complex formation – even in the absence of nucleotide –triggers significant conformational changes in DNA at the entry side, effectively priming the system for remodelling. During remodelling, flanking DNA enters the nucleosome in a continuous, gradual manner but exits in concerted 4–6 base-pair steps. This decoupling of entry- and exit-side translocation suggests that ATP-driven movement of entry-side DNA builds up strain inside the nucleosome that is subsequently released at the exit side by DNA expulsion.
We have also dissected the functional roles of auxiliary domains of CHD4 and demonstrate that CHD4 activity is regulated by both an N-terminal intrinsically disordered domain and a C-terminal DNA-binding autoinhibitory domain.
These data reveal unsuspected relationships between CHD4 and other chromatin remodelling enzymes. We propose a mechanism for nucleosome sliding based on these and published data.