NMR investigations on H2A-H2B heterodimer dynamics conferred by histone variant H2A.Z

H2A.Z, a highly conserved histone H2A variant in eukaryotes, plays critical roles in multiple nuclear events. H2A.Z forms a heterodimer with H2B when incorporated into nucleosomes. The heterodimer dynamics has been implicated in H2A.Z functions. To gain insights into H2A.Z dynamics, we analyzed yeast H2A.Z-H2B dimer (ZB) and yeast H2A-H2B dimer (AB) using solution NMR spectroscopy. First, we measured the ¹H-¹⁵N heteronuclear NOE ratio of ZB and showed that the H2A.Z αC-helix region (residues 100-118) undergoes less structure fluctuation than its H2A counterpart. Strikingly, substituting H2A residues G₉₉N₁₀₀V₁₀₁ with H2A.Z counterparts R₁₀₆A₁₀₇ reduced the fluctuation of H2A αC-helix, suggesting that H2A.Z dynamics play an important role in αC-helix extension and H2A.Z-chaperones recognition. We next measured the hydrogen-deuterium exchange (HX) rate of ZB and verified that the H2A.Z α2 helix and H2B α2, α3 helices are mostly protected. Notably, we observed nearly identical HX profiles for dimerized ZB and AB, suggesting that they have similar solution structures and dynamic characters. Together, our study gains first insight into H2A.Z-H2B dimer dynamics and sheds light on how its dynamics affect the structure and function of H2A.Z variant.