H2A histone-fold and DNA elements in nucleosome activate SWR1-mediated H2A.Z replacement in budding yeast

Abstract

The histone variant H2A.Z is a universal mark of gene promoters, enhancers, and regulatory elements in eukaryotic chromatin. The chromatin remodeler SWR1 mediates site-specific incorporation of H2A.Z by a multi-step histone replacement reaction, evicting histone H2A-H2B from the canonical nucleosome and depositing the H2A.Z-H2B dimer. Binding of both substrates, the canonical nucleosome and the H2A.Z-H2B dimer, is essential for activation of SWR1. We found that SWR1 primarily recognizes key residues within the α2 helix in the histone-fold of nucleosomal histone H2A, a region not previously known to influence remodeler activity. Moreover, SWR1 interacts preferentially with nucleosomal DNA at superhelix location 2 on the nucleosome face distal to its linker-binding site. Our findings provide new molecular insights on recognition of the canonical nucleosome by a chromatin remodeler and have implications for ATP-driven mechanisms of histone eviction and deposition.DOI: http://dx.doi.org/10.7554/eLife.06845.001

Structure and dynamics of the yeast SWR1-nucleosome complex

“…Interactions with Asp 91 and Glu 93 of the H2A acidic patch anchor this module firmly on the face of the octamer. The acidic patch has previously been shown to be important for SWR1 histone 3 of 8 exchange (17). Similarly, we observe a loss in histone exchange activity when Arp6/Swc6 is deleted ( Fig.…”

“…Multiple contacts are made with the histone core and DNA wrap. The Swr1 subunit ATPase domains are located at the canonical SHL2 position seen in the structures of most other remodelers (19,20) and consistent with SWR1-nucleosome footprinting studies (17). There is clear density for a bound nucleotide (ADP• BeF 3 ) at the ATP-binding site ( fig.…”

“…Biochemical data have shown that SWR1 prefers nucleosome substrates with overhangs on both sides, with at least one of these needing to be long [>60 base pairs (bp)] (17,21). We therefore used a canonical H2A-containing yeast nucleosome with overhangs on both sides (113N25), in the presence of the ATP analog ADP•BeF 3 , to prepare a complex suitable for structure determination by cryo-EM ( Fig.…”

INO80 exchanges H2A.Z for H2A by translocating on DNA proximal to histone dimers

“…Overlays of the protection patterns of nucleosomes alone and bound to INO80 revealed the regions where INO80 stably interacts with DNA. We found that unlike NURF, ISW2, ISW1a, SWI/SNF and SWR1; INO80 does not stably bind to SHL−2, or two DNA helical turns from the dyad axis3948. Instead, INO80 interacts with nucleosomal DNA at SHL −3, −5 and −6 as seen by DNA footprinting protections centred at −33, −53 and −63 nucleotides (nt) from the dyad axis (compare Fig.…”

Interdomain Communication of the Chd1 Chromatin Remodeler across the DNA Gyres of the Nucleosome

“…Previously, remodeling activities for several chromatin remodelers were shown to require intact DNA at the internal SHL2 site on the nucleosome, which is ~50 bp from the closest edge of the nucleosome (McKnight et al, 2011; Ranjan et al, 2015; Saha et al, 2005; Schwanbeck et al, 2004; Zofall et al, 2006). Cross-linking studies with ISWI and SWI/SNF remodelers demonstrated that the ATPase motor of the remodeler bound to SHL2 (Dang and Bartholomew, 2007; Dechassa et al, 2012); however, the photoactivatable cross-linkers in those studies originated from DNA and therefore did not provide sufficient information for uniquely orienting the protein domains on the nucleosome.…”