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Structure and nucleosome interaction of the yeast NuA4 and Piccolo–NuA4 histone acetyltransferase complexes

Nature Structural & Molecular Biology volume 18, pages 1196–1203 (2011)Cite this article

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Abstract

We have used EM and biochemistry to characterize the structure of NuA4, an essential yeast histone acetyltransferase (HAT) complex conserved throughout eukaryotes, and we have determined the interaction of NuA4 with the nucleosome core particle (NCP). The ATM-related Tra1 subunit, which is shared with the SAGA coactivator complex, forms a large domain joined to a second region that accommodates the catalytic subcomplex Piccolo and other NuA4 subunits. EM analysis of a NuA4–NCP complex shows the NCP bound at the periphery of NuA4. EM characterization of Piccolo and Piccolo–NCP provided further information about subunit organization and confirmed that histone acetylation requires minimal contact with the NCP. A small conserved region at the N terminus of Piccolo subunit enhancer of Polycomb-like 1 (Epl1) is essential for NCP interaction, whereas the subunit yeast homolog of mammalian Ing1 2 (Yng2) apparently positions Piccolo for efficient acetylation of histone H4 or histone H2A tails. Taken together, these results provide an understanding of the NuA4 subunit organization and the NuA4–NCP interactions.

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Figure 1: NuA4 subunit organization and EM characterization.
Figure 2: NuA4 subunit organization, interaction with the nucleosome and structural homology with SAGA.
Figure 3: Characterization of the Piccolo–nucleosome core particle complex by analytical ultracentrifugation and EM.
Figure 4: Epl1 N terminus drives binding to nucleosomes within NuA4, but Yng2 is required for acetylation.
Figure 5: Epl1 residues 51–72 are essential for the Piccolo-NCP interaction.

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Acknowledgements

This work was supported by US National Institutes of Health grants R01 GM67167 (F.J.A.), R01 GM060489 (S.T.) and R01 GM070662 (M.G.F.), and fellowship F31 GM086978 (J.R.C.), by a Canadian Institutes of Health Research grant MOP-14308 (J.C.) and fellowship (V.S.), and by a Canada Research Chair (J.C.). We also acknowledge the National Resource for Automated Macromolecular Microscopy.

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Authors and Affiliations

  1. Department of Cell Biology, The Scripps Research Institute, La Jolla, California, USA

    Johnathan R Chittuluru, Yuriy Chaban, Gang Cai & Francisco J Asturias

  2. Laval University Cancer Research Center, Hôtel-Dieu de Québec (CHUQ), Quebec City, Quebec, Canada

    Julie Monnet-Saksouk, Vasileia Sapountzi, Rhea T Utley, Myriam Cramet, Stephane Allard & Jacques Côté

  3. Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA

    Michael J Carrozza

  4. Department of Biochemistry and Molecular Biology, Center for Eukaryotic Gene Regulation, Pennsylvania State University, University Park, Pennsylvania, USA

    William Selleck, Jiehuan Huang & Song Tan

  5. Stowers Institute for Medical Research, Kansas City, Missouri, USA

    Jerry L Workman

  6. Department of Molecular and Cellular Biochemistry, Center for Structural Biology, University of Kentucky, Lexington, Kentucky, USA

    Michael G Fried

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  1. Johnathan R Chittuluru
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Contributions

M.J.C. and J.M.-S. expressed and purified NuA4 for EM analysis; J.M.-S. expressed and purified the SAGA complex; J.M.-S., R.T.U., V.S., M.C. and S.A. expressed and purified NuA4 and recombinant component subunits for biochemical analysis and performed all biochemical analyses of NuA4 and component subunits; W.S. produced the recombinant NCP; W.S. and J.H. expressed and purified all Piccolo–NuA4 variants and Piccolo–NuA4 in complex with the NCP; M.G.F. performed all analytical ultracentrifugation experiments; Y.C. collected EM data for NuA4 preserved in ice and calculated the RCT 3D reconstruction of NuA4 from stained particles; J.R.C. collected and analyzed all additional EM data and calculated all remaining structures for Piccolo–NuA4 and NuA4; G.C. performed initial quality inspection of 3D NuA4 structures with J.R.C. and F.J.A.; J.R.C., F.J.A., S.T. and J.C. discussed and interpreted all results; F.J.A. supervised all EM-based structural analysis; J.R.C. and F.J.A. wrote the manuscript with input from J.C. and S.T.

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Correspondence to Jacques Côté or Francisco J Asturias.

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Chittuluru, J., Chaban, Y., Monnet-Saksouk, J. et al. Structure and nucleosome interaction of the yeast NuA4 and Piccolo–NuA4 histone acetyltransferase complexes. Nat Struct Mol Biol 18, 1196–1203 (2011). https://doi.org/10.1038/nsmb.2128

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