Recognition of the inherently unstable H2A nucleosome by Swc2 is a major determinant for unidirectional H2A.Z exchange

Abstract

The multisubunit chromatin remodeler SWR1/SRCAP/p400 replaces the nucleosomal H2A-H2B dimer with the free-form H2A.Z-H2B dimer, but the mechanism governing the unidirectional H2A-to-H2A.Z exchange remains elusive. Here, we perform single-molecule force spectroscopy to dissect the disassembly/reassembly processes of the H2A nucleosome and H2A.Z nucleosome. We find that the N-terminal 1-135 residues of yeast SWR1 complex protein 2 (previously termed Swc2-Z) facilitate the disassembly of nucleosomes containing H2A but not H2A.Z. The Swc2-mediated nucleosome disassembly/reassembly requires the inherently unstable H2A nucleosome, whose instability is conferred by three H2A a2-helical residues, Gly47, Pro49, and Ile63, as they selectively weaken the structural rigidity of the H2A-H2B dimer. It also requires Swc2-ZN (residues 1-37) that directly anchors to the H2A nucleosome and functions in the SWR1-catalyzed H2A.Z replacement in vitro and yeast H2A.Z deposition in vivo. Our findings provide mechanistic insights into how the SWR1 complex discriminates between the H2A nucleosome and H2A.Z nucleosome, establishing a simple paradigm for the governance of unidirectional H2A.Z exchange.

H2A-H2B Histone Dimer Plasticity and Its Functional Implications

“…Certain effects of H2A.Z on nucleosome stability and functioning have been biochemically mapped to specific amino acids; however, the exact dynamical mechanisms are not yet completely clear. For instance, in yeast, remodeler SWR1 was previously shown to distinguish the H2A-NCP from the H2A.Z-NCP, and the inner region (N-end of α2-helix) was shown to be critical for this discrimination [ 39 , 40 ].…”

“…Recent experimental data for S. cerevisiae histones suggest that the differences between H2A and H2A.Z at two sites at the N-end of the α2-helix (G47K and P49A, which in humans correspond to G46T and P48A, see Figure 1 d) are responsible for altered thermal stability of the nucleosomes and the capability for the SWR1 remodeler in yeast to distinguish between canonical and H2A.Z-containing nucleosomes [ 39 , 40 ]. Although H2A.Z in S. cerevisiae has a different amino acid substitution at one position (G47K in yeast vs. G46T in humans), H2A.Z histones across all eukaryotes have a sequence where glycine and proline at the N-end of the α2-helix in canonical H2A are substituted for different amino acids [ 66 ], highlighting the potential functional importance of these substitutions.…”

“…By the example of H2A.Z-H2B dynamics analysis, we have shown that histone sequence also may affect the local dynamics of histone fold elements. Dai et al [ 40 ] have previously shown that substitutions of G47K and P49A in yeast H2A.Z with respect to canonical H2A increase dimer and nucleosome stability, which in turn contributes to the ability of SWR1 to discriminate between H2A and H2A.Z nucleosomes [ 39 ]. Similar amino acid substitutions of glycine and proline at the N-end of the α2-helix are found in H2A.Z across eukaryotes, including human H2A.Z that we have studied.…”

“…These residues are not exposed on the surface of the nucleosome. It has been suggested that changes in the H2A-H2B dynamics and stability due to these substitutions are, in fact, responsible for these effects [ 39 , 40 ]. Overall, we expect that other dynamical modes of functional significance exist within H2A-H2B dimers awaiting characterization.…”

“…Key structural elements are annotated below or on top of the sequences. Two positions on the alignment (highlighted in cyan frames) correspond to analog positions of H2A/H2A.Z substitutions in yeast affecting nucleosome stability and SWR1 activity [ 39 , 40 ]. ▼ and ▽ mark the histone tails’ truncation sites in NCP and dimer systems’ simulations, respectively.…”