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

Abstract

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.

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Figure 1: 3D structures of Rtt106 dimeric and double PH domains and their interaction with histones.
Figure 2: Identification of a K56ac-binding cleft in Rtt106 and model of Rtt106 in complex with K56-acetylated (H3–H4)2.
Figure 3: Effects of Rtt106PH mutations on H3K56ac interaction.
Figure 4: Effects of Rtt106 mutations on HMR silencing and genome stability.

Accession codes

Primary accessions

Biological Magnetic Resonance Data Bank

Protein Data Bank

Data deposits

The atomic coordinates and structure factors orNMR restraints of Rtt106DD, Rtt106PH, Rtt106PHL and Rtt106PH–acetyl-histamine have been deposited with the Protein Data Bank under accession codes 2LH0, 3FSS, 3TVV and 3TW1, respectively. The NMR chemical shifts of Rtt106 (residues 1–67) have been deposited in the Biological Magnetic Resonance Bank with the accession code 17832.

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Acknowledgements

We are grateful to N. Juranić, S. Macura and T. Burghardt for experimental advice, Y. Kim for assistance with X-ray data collection, Z. Zhang for suggestions on chemical synthesis, and K. Luger and A. Hieb for advice on the preparation of histones. We acknowledge the use of synchrotron beamlines 19BM and 19ID of the Structural Biology Center at Argonne National Laboratory’s APS, supported by the US Department of Energy, Basic Energy Sciences, Office of Science, under contract no. W-31-109-ENG-38. This work was funded in part by National Institutes of Health grants to Z.Z. and G.M.

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Q.H. carried out the NMR spectroscopy experiments, prepared methylthiocarbonyl-aziridine and acetylated H3–H4, and performed the ITC measurements and analysis with assistance from G.M.; D.S. obtained crystals of the Rtt106 constructs, performed the X-ray diffraction measurements and solved the structures. Q.L. did the in vivo experiments. G.C. helped with the NMR experiments and ITC data analysis, A.F. and B.A.D. purified Rtt106 for initial crystal screening. J.R.T. worked on the refinement of crystal structures, M.V.B. contributed extensively to plasmid design, mutagenesis and protein preparations. G.M. and Z.Z. supervised the research. G.M. wrote the manuscript. All authors contributed in editing the manuscript.

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Correspondence to Zhiguo Zhang or Georges Mer.

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The authors declare no competing financial interests.

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This file contains a Supplementary Discussion, Supplementary Figures 1-14 with legends, Supplementary Tables 1-4 and Supplementary References. (PDF 14606 kb)

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Su, D., Hu, Q., Li, Q. et al. Structural basis for recognition of H3K56-acetylated histone H3–H4 by the chaperone Rtt106. Nature 483, 104–107 (2012). https://doi.org/10.1038/nature10861

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