Mechanism of chromatin remodelling revealed by the Snf2-nucleosome structure

Abstract

Chromatin remodellers are helicase-like, ATP-dependent enzymes that alter chromatin structure and nucleosome positions to allow regulatory proteins access to DNA. Here we report the cryo-electron microscopy structure of chromatin remodeller Switch/sucrose non-fermentable (SWI2/SNF2) from Saccharomyces cerevisiae bound to the nucleosome. The structure shows that the two core domains of Snf2 are realigned upon nucleosome binding, suggesting activation of the enzyme. The core domains contact each other through two induced Brace helices, which are crucial for coupling ATP hydrolysis to chromatin remodelling. Snf2 binds to the phosphate backbones of one DNA gyre of the nucleosome mainly through its helicase motifs within the major domain cleft, suggesting a conserved mechanism of substrate engagement across different remodellers. Snf2 contacts the second DNA gyre via a positively charged surface, providing a mechanism to anchor the remodeller at a fixed position of the nucleosome. Snf2 locally deforms nucleosomal DNA at the site of binding, priming the substrate for the remodelling reaction. Together, these findings provide mechanistic insights into chromatin remodelling.

Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome

“…These are the only direct contacts with histone components of the nucleosome. The contact with the H4 tails is conserved in mtISWI and Snf2 (Liu et al, 2017; Yan et al, 2016). D729 and E669 are conserved across all classes of remodelling enzyme but D725 is not as well conserved in Snf2-related enzymes (Figure 2—figure supplement 4B).…”

“…To do this we first align the ATPase lobes of Chd1 individually with NS3. The ATPase lobes of Chd1 like other Snf2 related proteins contain additional helices not conserved with NS3 (Dürr et al, 2005; Liu et al, 2017; Thomä et al, 2005). As a result, the alignment is restricted to conserved helices.…”

“…As these motifs are intimately associated with motif Ia they would be anticipated to undergo a similar ratcheting motion with respect to the contacts made by lobe 2. Secondly, the ATPase lobes of Chd1 like those of Snf2 contain additional helices including the protrusions to the helical lobes and the brace helix that are unique to chromatin remodelling enzymes (Figure 6A) (Farnung et al, 2017; Flaus et al, 2006; Liu et al, 2017). These extend the binding cleft between the ATPase lobes and make additional contacts with both DNA strands.…”

“…The structure of a fragment of the yeast Snf2 protein bound to a nucleosome revealed contacts between ATPase lobe one with DNA at SHL2 and the adjacent DNA gyre at SHL 6 (Liu et al, 2017) (Figure 6—figure supplement 2A). The basic surface of lobe one responsible for this interaction is not conserved in Chd1, and the acidic residues D464 and E468 make a similar interaction with DNA unlikely.…”

“…Chd1 enzyme engages nucleosomes in a conformation in which the SANT and SLIDE domains bind linker DNA, while the ATPase domains engage DNA at super helical location (SHL) 2 (Nodelman et al, 2017; Sundaramoorthy et al, 2017). Higher resolution structures of Chd1 (Farnung et al, 2017), Snf2 (Liu et al, 2017) and INO80 (Ayala et al, 2018; Eustermann et al, 2018) show that the ATPase domains make contacts with DNA via residues that are conserved in ancestral single-stranded ATPases and some unique to Snf2-related ATPases. The binding of the Chd1 DNABD unravels two turns of DNA from the surface of nucleosomes in a nucleotide-stimulated reaction (Farnung et al, 2017; Sundaramoorthy et al, 2017).…”