UCSF

Chromatin remodelers are molecular motors that reposition and restructure nucleosomes to regulate gene expression and genome organization. The human ATP-dependent chromatin assembly factor (ACF) is a dimeric chromatin remodeler that evenly spaces nucleosomes to promote the formation of silent heterochromatin. Two copies of its ATPase subunit, SNF2h, bind opposite sides of a nucleosome, but how the two protomers work together remains poorly understood.

Central to the nucleosome spacing activity of ACF is the ability of SNF2h to equalize the length of DNA flanking either side of a nucleosome. SNF2h senses flanking DNA length via its conserved HAND-SANT-SLIDE (HSS) domain, yet it is unclear 1) how this interaction contributes to remodeling, and 2) whether or how the HSS communicates with the ATPase domain.

In this work, we address these questions with a combination of biochemical, biophysical and protein engineering methods. Using covalently connected SNF2h dimers we show that dimerization accelerates remodeling and that the HSS contributes to communication between protomers in trans. Moreover, we find that the state of the ATPase domain influences the function of the HSS domain within the same protomer in cis. Using thermodynamic analyses and new FRET-based assays, we further examine how nucleotide state regulates interactions between the HSS domain and the nucleosome. We identify a large, nucleotide-dependent conformational change in SNF2h: in one conformation the HSS binds flanking DNA, and in another conformation the HSS retracts to engage the nucleosome core. Finally, we examine the role of a recently identified regulatory motif, termed NegC, in nucleosome remodeling by SNF2h. We find that mutating NegC impairs flanking DNA length sensing, abolishes mononucleosome centering, and reduces the dependence of SNF2h activity on the histone H4 tail.

Based on these new results and previously published work, we propose a model in which DNA length sensing and translocation are performed by two distinct conformational states of SNF2h. We speculate that the ATP-dependent switch between DNA length-sensing and translocation-competent forms of the enzyme represents a rate-limiting regulatory step that enables nucleosome spacing by ACF. Such separation of function suggests that these two activities could be independently regulated to fine-tune remodeling outcomes.