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J. Biol. Chem., Vol. 282, Issue 10, 7641-7655, March 9, 2007

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Organismal Differences in Post-translational Modifications in Histones H3 and H4^*

Benjamin A. Garcia¹², Sandra B. Hake¹³, Robert L. Diaz, Monika Kauer⁴, Stephanie A. Morris^¶, Judith Recht⁵, Jeffrey Shabanowitz, Nilamadhab Mishra^||, Brian D. Strahl^¶6, C. David Allis⁷, and Donald F. Hunt^**8

From the Department of Chemistry, University of Virginia, Charlottesville, Virginia 22901, the Laboratory of Chromatin Biology, The Rockefeller University, New York, New York 10021, the ^¶Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, the ^||Section on Rheumatology and Clinical Immunology, Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, and the ^**Department of Pathology, Health Sciences Center, University of Virginia, Charlottesville, Virginia 22908

Post-translational modifications (PTMs) of histones play an important role in many cellular processes, notably gene regulation. Using a combination of mass spectrometric and immunobiochemical approaches, we show that the PTM profile of histone H3 differs significantly among the various model organisms examined. Unicellular eukaryotes, such as Saccharomyces cerevisiae (yeast) and Tetrahymena thermophila (Tet), for example, contain more activation than silencing marks as compared with mammalian cells (mouse and human), which are generally enriched in PTMs more often associated with gene silencing. Close examination reveals that many of the better-known modified lysines (Lys) can be either methylated or acetylated and that the overall modification patterns become more complex from unicellular eukaryotes to mammals. Additionally, novel species-specific H3 PTMs from wild-type asynchronously grown cells are also detected by mass spectrometry. Our results suggest that some PTMs are more conserved than previously thought, including H3K9me1 and H4K20me2 in yeast and H3K27me1, -me2, and -me3 in Tet. On histone H4, methylation at Lys-20 showed a similar pattern as H3 methylation at Lys-9, with mammals containing more methylation than the unicellular organisms. Additionally, modification profiles of H4 acetylation were very similar among the organisms examined.

Received for publication, August 17, 2006 , and in revised form, December 19, 2006.

^* This work was supported in part by National Institutes of Health Grants GM 40922 (to C. D. A.), GM 37537 (to D. F. H.), and GM 68088 (to B. D. S.), by the Ford Foundation (to B. A. G. and S. A. M.), and by The Rockefeller University ("Women & Science Fellowship to S. B. H.). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

The on-line version of this article (available at http://www.jbc.org) contains supplemental Figs. S1-S6 and supplemental data pages 1-34.

¹ Both authors contributed equally to the work.

² Present address: Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Illinois 61801.

³ Present address: Adolf-Butenandt-Institut, Molekularbiologie, Ludwig-Maximilians-Universität, 80336 München, Germany.

⁴ Present address: Research Institute of Molecular Pathology, The Vienna Biocenter, A-1030 Vienna, Austria.

⁵ Present address: Dept. of Oncological Sciences, Mount Sinai School of Medicine, New York, NY 10029.

⁶ A Pew Scholar in the Biomedical Sciences.

⁷ To whom correspondence may be addressed: Laboratory of Chromatin Biology, The Rockefeller University, Box 78, 1230 York Ave., New York, NY 10021. Tel.: 212-327-7839; Fax: 212-327-7849; E-mail: alliscd{at}rockefeller.edu.

⁸ To whom correspondence may be addressed. Tel.: 434-924-3610; Fax: 434-982-2781; E-mail: dfh{at}virginia.edu.

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