Structural and Functional Conservation of the NuA4 Histone Acetyltransferase Complex from Yeast to Humans

Abstract

The NuA4 histone acetyltransferase (HAT) multisubunit complex is responsible for acetylation of histone H4 and H2A N-terminal tails in yeast. Its catalytic component, Esa1, is essential for cell cycle progression, gene-specific regulation and has been implicated in DNA repair. Almost all NuA4 subunits have clear homologues in higher eukaryotes, suggesting that the complex is conserved throughout evolution to metazoans. We demonstrate here that NuA4 complexes are indeed present in human cells. Tip60 and its splice variant Tip60b/PLIP were purified as stable HAT complexes associated with identical polypeptides, with 11 of the 12 proteins being homologs of yeast NuA4 subunits. This indicates a highly conserved subunit composition and the identified human proteins underline the role of NuA4 in the control of mammalian cell proliferation. ING3, a member of the ING family of growth regulators, links NuA4 to p53 function which we confirmed in vivo. Proteins specific to the human NuA4 complexes include ruvB-like helicases and a bromodomain-containing subunit linked to ligand-dependent transcription activation by the thyroid hormone receptor. We also demonstrate that subunits MRG15 and DMAP1 are present in distinct protein complexes harboring histone deacetylase and SWI2-related ATPase activities, respectively. Finally, analogous to yeast, a recombinant trimeric complex formed by Tip60, EPC1, and ING3 is sufficient to reconstitute robust nucleosomal HAT activity in vitro. In conclusion, the NuA4 HAT complex is highly conserved in eukaryotes, in which it plays primary roles in transcription, cellular response to DNA damage, and cell cycle control.

We are grateful to G. Chinnadurai for Tip60 cDNA, B. Séraphin for the TAP system plasmids, Y. Makino for anti-Tip49a/b(RUVBL1/2), Y. Matsuoka for anti-MRG15, A. Munnia and E. Meese for anti-GAS41, M. Takahashi for anti-EPC1, W. Wang for anti-BAF53a and anti-HDAC2, and A. Anderson for the p53 expression vector. We thank Marie Martineau for help in cloning, Marc Bergeron for the human kidney cDNA bank, Frédéric Beaulieu for gamma irradiation of cells, Vincent Roy and Manuel Caruso for help with retrovirus, Josée Lavoie's lab for help and advice in cell culture and transfections, Rhea Utley for critical reading of the manuscript, and members of our lab for fruitful discussions.

This study was supported by grants from the Cancer Research Society, Inc., GénomeCanada/GénomeQuébec, and the Canadian Institutes of Health Research (CIHR) to J.C. and from the National Institutes of Health to S.T. Y.D. was a Natural Sciences and Engineering Research Council graduate student and currently holds a CIHR/Canada Graduate scholarship. S.T. is a Pew Scholar in the Biomedical Sciences. J.C. is a CIHR Investigator.