Quantitative Analysis of Histone Modifications: Formaldehyde Is a Source of Pathological N6-Formyllysine That Is Refractory to Histone Deacetylases

PLoS Genetics

Volumn 9, Issue 2, 2013, Pages

  Edrissi, Bahar ^a   Taghizadeh, Koli ^a   Dedon, Peter C ^a  

^a USA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FORMALDEHYDE; FORMYLLYSINE; HISTONE DEACETYLASE 1; HISTONE DEACETYLASE 2; HISTONE DEACETYLASE 3; HISTONE DEACETYLASE INHIBITOR; LYSINE; SIRTUIN 1; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; ENZYME ACTIVITY; ENZYME REGULATION; ENZYME SUBSTRATE; HISTONE ACETYLATION; HISTONE MODIFICATION; HUMAN; HUMAN CELL; ISOTOPE LABELING; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN STRUCTURE; QUANTITATIVE ANALYSIS; STRUCTURE ANALYSIS;

ACETYLATION; FORMALDEHYDE; GENE EXPRESSION; HISTONE DEACETYLASES; HISTONES; HUMANS; LYSINE; METHYLATION; PROTEIN PROCESSING, POST-TRANSLATIONAL; RESPIRATORY HYPERSENSITIVITY;

EID: 84874770498     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1003328     Document Type: Article

References (41)

1. Levine RL, (2002) Carbonyl modified proteins in cellular regulation, aging, and disease. Free Radic Biol Med 32: 790-796.
2. Jacobs AT, Marnett LJ, (2010) Systems analysis of protein modification and cellular responses induced by electrophile stress. Acc Chem Res 43: 673-683.
3. Thornalley PJ, (2008) Protein and nucleotide damage by glyoxal and methylglyoxal in physiological systems-role in ageing and disease. Drug Metabol Drug Interact 23: 125-150.
4. Dedon PC, (2008) The chemical toxicology of 2-deoxyribose oxidation in DNA. Chem Res Toxicol 21: 206-219.
5. Vana L, Kanaan NM, Hakala K, Weintraub ST, Binder LI, (2011) Peroxynitrite-induced nitrative and oxidative modifications alter tau filament formation. Biochemistry 50: 1203-1212.
6. Codreanu SG, Zhang B, Sobecki SM, Billheimer DD, Liebler DC, (2009) Global analysis of protein damage by the lipid electrophile 4-hydroxy-2-nonenal. Mol Cell Proteomics 8: 670-680.
7. Tallman KA, Kim HY, Ji JX, Szapacs ME, Yin H, et al. (2007) Phospholipid-protein adducts of lipid peroxidation: synthesis and study of new biotinylated phosphatidylcholines. Chem Res Toxicol 20: 227-234.
8. Prasad A, Bekker P, Tsimikas S, (2012) Advanced Glycation Endproducts and Diabetic Cardiovascular Disease. Cardiol Rev 20: 177-183.
9. Jiang T, Zhou X, Taghizadeh K, Dong M, Dedon PC, (2007) N-formylation of lysine in histone proteins as a secondary modification arising from oxidative DNA damage. Proc Natl Acad Sci U SA 104: 60-65.
10. Wisniewski JR, Zougman A, Mann M, (2008) Nepsilon-formylation of lysine is a widespread post-translational modification of nuclear proteins occurring at residues involved in regulation of chromatin function. Nucleic Acids Res 36: 570-577.
11. LeRoy G, Weston JT, Zee BM, Young NL, Plazas-Mayorca MD, et al. (2009) Heterochromatin protein 1 is extensively decorated with histone code-like post-translational modifications. Mol Cell Proteomics 8: 2432-2442.
12. Pesavento JJ, Kim YB, Taylor GK, Kelleher NL, (2004) Shotgun annotation of histone modifications: a new approach for streamlined characterization of proteins by top down mass spectrometry. J Am Chem Soc 126: 3386-3387.
13. Felsenfeld G, Groudine M, (2003) Controlling the double helix. Nature 421: 448-453.
14. Chi P, Allis CD, Wang GG, (2010) Covalent histone modifications-miswritten, misinterpreted and mis-erased in human cancers. Nat Rev Cancer 10: 457-469.
15. Rando OJ, (2012) Combinatorial complexity in chromatin structure and function: revisiting the histone code. Curr Opin Genet Dev 22: 148-55.
16. Kouzarides T, (2007) Chromatin modifications and their function. Cell 128: 693-705.
17. Siuti N, Roth MJ, Mizzen CA, Kelleher NL, Pesavento JJ, (2006) Gene-specific characterization of human histone H2B by electron capture dissociation. J Proteome Res 5: 233-239.
18. Garcia BA, Barber CM, Hake SB, Ptak C, Turner FB, et al. (2005) Modifications of human histone H3 variants during mitosis. Biochemistry 44: 13202-13213.
19. Lu K, Moeller B, Doyle-Eisele M, McDonald J, Swenberg JA, (2011) Molecular dosimetry of N2-hydroxymethyl-dG DNA adducts in rats exposed to formaldehyde. Chem Res Toxicol 24: 159-161.
20. Zhang L, Freeman LE, Nakamura J, Hecht SS, Vandenberg JJ, et al. (2010) Formaldehyde and leukemia: epidemiology, potential mechanisms, and implications for risk assessment. Environ Mol Mutagen 51: 181-191.
21. Le Curieux F, Pluskota D, Munter T, Sjoholm R, Kronberg L, (2000) Identification of fluorescent 2′-deoxyadenosine adducts formed in reactions of conjugates of malonaldehyde and acetaldehyde, and of malonaldehyde and formaldehyde. Chem Res Toxicol 13: 1228-1234.
22. Begley TJ, Samson LD, (2003) AlkB mystery solved: oxidative demethylation of N1-methyladenine and N3-methylcytosine adducts by a direct reversal mechanism. Trends Biochem Sci 28: 2-5.
23. Shi Y, Whetstine JR, (2007) Dynamic regulation of histone lysine methylation by demethylases. Mol Cell 25: 1-14.
24. Pasqualini JR, Mercat P, Giambiagi N, (1989) Histone acetylation decreased by estradiol in the MCF-7 human mammary cancer cell line. Breast Cancer Res Treat 14: 101-105.
25. Byvoet P, Barber M, Amidei K, Lowell N, Trudeau W, (1986) Effect of exogenous histone H5 on integration of histone H1 in rat liver chromatin. Correlations with aberrant epsilon-N-methylation of histone H1. Biochim Biophys Acta 867: 163-175.
26. Wu M, Allis CD, Richman R, Cook RG, Gorovsky MA, (1986) An intervening sequence in an unusual histone H1 gene of Tetrahymena thermophila. Proc Natl Acad Sci USA 83: 8674-8678.
27. Strahl BD, Allis CD, (2000) The language of covalent histone modifications. Nature 403: 41-45.
28. de Ruijter AJ, van Gennip AH, Caron HN, Kemp S, van Kuilenburg AB, (2003) Histone deacetylases (HDACs): characterization of the classical HDAC family. Biochem J 370: 737-749.
29. Hildmann C, Riester D, Schwienhorst A, (2007) Histone deacetylases-an important class of cellular regulators with a variety of functions. Appl Microbiol Biotechnol 75: 487-497.
30. Hake SB, Xiao A, Allis CD, (2004) Linking the epigenetic 'language' of covalent histone modifications to cancer. Br J Cancer 90: 761-769.
31. Chen L, (2011) Medicinal chemistry of sirtuin inhibitors. Curr Med Chem 18: 1936-1946.
32. Dokmanovic M, Clarke C, Marks PA, (2007) Histone deacetylase inhibitors: overview and perspectives. Mol Cancer Res 5: 981-989.
33. Tyihak E, Trezl L, Kolonits P, (1985) The isolation of Nepsilon-formyl-L-lysine from the reaction between formaldehyde and L-lysine and its identification by OPLC and NMR spectroscopy. J Pharm Biomed Anal 3: 343-349.
34. Oses-Prieto JA, Zhang X, Burlingame AL, (2007) Formation of epsilon-formyllysine on silver-stained proteins: implications for assignment of isobaric dimethylation sites by tandem mass spectrometry. Mol Cell Proteomics 6: 181-192.
35. Luka Z, Moss F, Loukachevitch LV, Bornhop DJ, Wagner C, (2011) Histone demethylase LSD1 is a folate-binding protein. Biochemistry 50: 4750-4756.
36. Humans IWGotEoCRt (2006) Formaldehyde, 2-butoxyethanol and 1-tert-butoxypropan-2-ol. IARC Monogr Eval Carcinog Risks Hum 88: 1-478.
37. Zhang L, Tang X, Rothman N, Vermeulen R, Ji Z, et al. (2010) Occupational exposure to formaldehyde, hematotoxicity, and leukemia-specific chromosome changes in cultured myeloid progenitor cells. Cancer Epidemiol Biomarkers Prev 19: 80-88.
38. Monticello TM, Swenberg JA, Gross EA, Leininger JR, Kimbell JS, et al. (1996) Correlation of regional and nonlinear formaldehyde-induced nasal cancer with proliferating populations of cells. Cancer Res 56: 1012-1022.
39. Swenberg JA, Kerns WD, Mitchell RI, Gralla EJ, Pavkov KL, (1980) Induction of squamous cell carcinomas of the rat nasal cavity by inhalation exposure to formaldehyde vapor. Cancer Res 40: 3398-3402.
40. Kerns WD, Pavkov KL, Donofrio DJ, Gralla EJ, Swenberg JA, (1983) Carcinogenicity of formaldehyde in rats and mice after long-term inhalation exposure. Cancer Res 43: 4382-4392.
41. Boyne MT 2nd, Pesavento JJ, Mizzen CA, Kelleher NL, (2006) Precise characterization of human histones in the H2A gene family by top down mass spectrometry. J Proteome Res 5: 248-253.