Preferential Binding of the Histone (H3-H4)2 Tetramer by NAP1 Is Mediated by the Amino-terminal Histone Tails

Abstract

The yeast nucleosome assembly protein 1 (yNAP1) participates in many diverse activities, such as the assembly of newly synthesized DNA into chromatin and the rearrangement of nucleosomes during transcriptional activation. yNAP1 does not require ATP hydrolysis to perform these functions and is a valuable tool for in vitro chromatin assembly. Using recombinant histone complexes, we show that yNAP1 has a preference for binding the (H3-H4) 2 tetramer over the (H2A-H2B) dimer. We find that the loss of the histone tails abrogates this preference for H3 and H4, and we demonstrate a direct interaction between yNAP1 and the amino-terminal tails of H3 and H4. yNAP1 binds to one histone fold domain, thus specifying the stoichiometry of the complexes formed with the histone dimer and tetramer. Finally, we provide evidence that the acidic carboxyl-terminal region of yNAP1, although dispensable for nucleosome assembly in vitro, contributes to binding via structure-independent electrostatic interactions. Our results are consistent with recent mechanistic investigations of NAP1 and expand our understanding of the histone chaperone family of assembly factors.

TTLL10 is a protein polyglycylase that can modify nucleosome assembly protein 1

“…Inspection of the three-dimensional structure of NAP1 suggests that the acidic surface of the NAP1 dimer contributes to the interaction between NAP1 and histones [20]. The C-terminal acidic domain participates in the interaction [21]. Addition of poly-glycine chains to the C-terminus could block the acidic effect, either by steric hindrance of the electrostatic charge, or even simpler by preventing the acidification caused by polyglutamylation as the modification sites were close to each other.…”

Histone chaperones in nucleosome eviction and histone exchange

“…Chz1, for example, appears to preferentially bind H2A.Z/H2B over H2A/H2B [40]. On the other side of the spectrum is NAP1, which binds all histones and even H1 rather non-discriminately, yet with high affinity [41]. To our knowledge no definitive measurements exist on the affinities or association/dissociation rate constants for any chaperone binding to any histone; these are required as an important piece of the puzzle to establish the mechanism for chaperone -mediated nucleosome dissociation and assembly.…”

The structure of nucleosome assembly protein 1

“…Yeast NAP-1 (perhaps the best-characterized of all members of the NAP-1 family) is a 48-kDa polypeptide that binds H2A-H2B and H3-H4 and mediates nucleosome assembly in vitro (3,7). Structural and functional analyses of the central domain of yeast NAP-1 (residues 74-365) have shown that this region retains a native-like structure and functions normally in nucleosome assembly (7,8).…”

“…Yeast NAP-1 (perhaps the best-characterized of all members of the NAP-1 family) is a 48-kDa polypeptide that binds H2A-H2B and H3-H4 and mediates nucleosome assembly in vitro (3,7). Structural and functional analyses of the central domain of yeast NAP-1 (residues 74-365) have shown that this region retains a native-like structure and functions normally in nucleosome assembly (7,8). Sedimentation equilibrium experiments revealed that yNAP-1 exists as a stable dimer and self-associated oligomers in solution; monomers are never observed in the absence of denaturing agents (9,10).…”