Structural basis for recognition of H3K56-acetylated histone H3–H4 by the chaperone Rtt106

Abstract

Direct binding of Rtt106 to H3K56-acetylated (H3–H4)2 histone tetramers contributes to nucleosome assembly with implications for DNA replication, gene silencing and maintenance of genomic stability. The acetylation of lysine 56 of histone H3 (H3K56ac) has been implicated in the control of nucleosome assembly during DNA replication and repair, and the yeast histone chaperone Rtt106 contributes to histone deposition during replication. Here, structural and biochemical experiments reveal how Rtt106 interacts with the H3–H4 dimer through a combinatorial recognition mechanism requiring the tandem PH domains of Rtt106. Acetylated H3K56 serves to enhance the affinity of the interaction, apparently by leading to increased flexibility of the H3 amino-terminus. Dynamic variations in the structure of chromatin influence virtually all DNA-related processes in eukaryotes and are controlled in part by post-translational modifications of histones1,2,3. One such modification, the acetylation of lysine 56 (H3K56ac) in the amino-terminal α-helix (αN) of histone H3, has been implicated in the regulation of nucleosome assembly during DNA replication and repair, and nucleosome disassembly during gene transcription4,5,6,7,8,9,10. In Saccharomyces cerevisiae, the histone chaperone Rtt106 contributes to the deposition of newly synthesized H3K56ac-carrying H3–H4 complex on replicating DNA5, but it is unclear how Rtt106 binds H3–H4 and specifically recognizes H3K56ac as there is no apparent acetylated lysine reader domain in Rtt106. Here, we show that two domains of Rtt106 are involved in a combinatorial recognition of H3–H4. An N-terminal domain homodimerizes and interacts with H3–H4 independently of acetylation while a double pleckstrin-homology (PH) domain binds the K56-containing region of H3. Affinity is markedly enhanced upon acetylation of K56, an effect that is probably due to increased conformational entropy of the αN helix of H3. Our data support a mode of interaction where the N-terminal homodimeric domain of Rtt106 intercalates between the two H3–H4 components of the (H3–H4)2 tetramer while two double PH domains in the Rtt106 dimer interact with each of the two H3K56ac sites in (H3–H4)2. We show that the Rtt106–(H3–H4)2 interaction is important for gene silencing and the DNA damage response.