title: Measurement of acetylation turnover at distinct lysines in human histones identifies long-lived acetylation sites.
abstract: Histone acetylation has long been determined as a highly dynamic modification associated with open chromatin and transcriptional activation. Here we develop a metabolic labelling scheme using stable isotopes to study the kinetics of acetylation turnover at 19 distinct lysines on histones H3, H4 and H2A. Using human HeLa S3 cells, the analysis reveals 12 sites of histone acetylation with fast turnover and 7 sites stable over a 30 h experiment. The sites showing fast turnover (anticipated from classical radioactive measurements of whole histones) have half-lives between ~1-2 h. To support this finding, we use a broad-spectrum deacetylase inhibitor to verify that only fast turnover sites display 2-10-fold increases in acetylation whereas long-lived sites clearly do not. Most of these stable sites lack extensive functional studies or localization within global chromatin, and their role in non-genetic mechanisms of inheritance is as yet unknown.
authors.affiliation: Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA.
authors.forename: Yupeng
authors.initials: Y
authors.lastname: Zheng
authors.forename: Paul M
authors.initials: PM
authors.lastname: Thomas
authors.forename: Neil L
authors.initials: NL
authors.lastname: Kelleher
mesh_terms: D000107:Acetylation; D002843:Chromatin / Q000378:metabolism; D015894:Genome, Human; D006207:Half-Life; D006367:HeLa Cells; D056572:Histone Deacetylase Inhibitors / Q000494:pharmacology; D006657:Histones / Q000037:antagonists & inhibitors / Q000235:genetics / Q000378:metabolism*; D006801:Humans; D007553:Isotope Labeling; D007700:Kinetics; D008239:Lysine / Q000378:metabolism; D011499:Protein Processing, Post-Translational; D013997:Time Factors
chemical_list: D002843:Chromatin; D056572:Histone Deacetylase Inhibitors; D006657:Histones; D008239:Lysine
references.citation: Brief Funct Genomics. 2013 May;12(3):231-43
references.pmid: 23325510
references.citation: Cell. 2009 Sep 4;138(5):1019-31
references.pmid: 19698979
references.citation: EMBO Rep. 2011 Dec 23;13(1):60-7
references.pmid: 22056817
references.citation: Annu Rev Biochem. 2011;80:473-99
references.pmid: 21529160
references.citation: Science. 2009 May 22;324(5930):1076-80
references.pmid: 19461003
references.citation: Curr Biol. 2006 Jul 11;16(13):1280-9
references.pmid: 16815704
references.citation: J Biol Chem. 2010 Oct 22;285(43):32778-32786
references.pmid: 20699226
references.citation: Annu Rev Biochem. 1979;48:159-91
references.pmid: 382983
references.citation: Nat Genet. 2008 Jul;40(7):897-903
references.pmid: 18552846
references.citation: Nature. 2009 May 7;459(7243):113-7
references.pmid: 19270680
references.citation: Microbiol Mol Biol Rev. 2000 Jun;64(2):435-59
references.pmid: 10839822
references.citation: Biochem J. 1988 Feb 15;250(1):241-5
references.pmid: 3355515
references.citation: Nat Methods. 2010 Aug;7(8):631-3
references.pmid: 20639867
references.citation: Mol Cell Biol. 2008 Jan;28(1):468-86
references.pmid: 17967882
references.citation: Science. 2007 May 18;316(5827):1050-4
references.pmid: 17510366
references.citation: Biochem Cell Biol. 2002;80(3):363-78
references.pmid: 12123289
references.citation: J Biol Chem. 2010 Nov 19;285(47):36267-74
references.pmid: 20813845
references.citation: PLoS Genet. 2011 Mar;7(3):e1001354
references.pmid: 21483810
references.citation: Sci Rep. 2012;2:220
references.pmid: 22355734
references.citation: Annu Rev Biochem. 2007;76:75-100
references.pmid: 17362198
references.citation: Anal Chem. 2008 May 1;80(9):3422-30
references.pmid: 18338905
references.citation: Annu Rev Biochem. 2009;78:273-304
references.pmid: 19355820
references.citation: Nat Protoc. 2007;2(4):933-8
references.pmid: 17446892
references.citation: Mol Cell. 2006 Jul 7;23(1):109-19
references.pmid: 16818235
references.citation: Cell. 2009 Apr 17;137(2):259-72
references.pmid: 19379692
references.citation: J Biol Chem. 1980 Oct 10;255(19):9110-6
references.pmid: 7410415
references.citation: Proc Natl Acad Sci U S A. 2012 Aug 21;109(34):13549-54
references.pmid: 22869745
references.citation: J Biol Chem. 2010 Jan 29;285(5):3341-50
references.pmid: 19940157
references.citation: Epigenetics Chromatin. 2010 Oct 20;3(1):18
references.pmid: 20961410
references.citation: Nat Rev Mol Cell Biol. 2012 Jun 22;13(7):436-47
references.pmid: 22722606
references.citation: J Am Soc Mass Spectrom. 2000 Jan;11(1):78-82
references.pmid: 10631667
references.citation: Bioinformatics. 2010 Apr 1;26(7):966-8
references.pmid: 20147306
references.citation: Mol Cell Biol. 2012 Jul;32(13):2503-14
references.pmid: 22547680
references.citation: Biochem J. 1988 Feb 15;250(1):233-40
references.pmid: 2451508