Chemical proteomics approaches to examine novel histone posttranslational modifications

Current Opinion in Chemical Biology

Volumn 24, Issue , 2015, Pages 80-90

  Li, Xin ^a   Li, Xiang David ^a  

^a UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE; HISTONE H2A; HISTONE H3; LYSINE; RIBOSOME DNA;

ACYLATION; CELL FUNCTION; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HISTONE ACETYLATION; HISTONE METHYLATION; HISTONE MODIFICATION; HISTONE UBIQUITINATION; HUMAN; MASS SPECTROMETRY; PROTEIN ANALYSIS; PROTEIN CROSS LINKING; PROTEIN PROCESSING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTEOMICS; REGULATORY MECHANISM; REVIEW; ANIMAL; CHEMISTRY; METABOLISM; PROCEDURES;

ANIMALS; HISTONES; HUMANS; MASS SPECTROMETRY; PROTEIN INTERACTION MAPPING; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEOMICS;

EID: 84919372537     PISSN: 13675931     EISSN: 18790402     Source Type: Journal    
DOI: 10.1016/j.cbpa.2014.10.015     Document Type: Review

References (69)

1. Luger K., Mader A.W., Richmond R.K., Sargent D.F., Richmond T.J. Crystal structure of the nucleosome core particle at 2.8Å resolution. Nature 1997, 389:251-260.
2. Zentner G.E., Henikoff S. Regulation of nucleosome dynamics by histone modifications. Nat Struct Mol Biol 2013, 20:259-266.
3. Suganuma T., Workman J.L. Signals and combinatorial functions of histone modifications. Annu Rev Biochem 2011, 80:473-499.
4. Patel D.J., Wang Z. Readout of epigenetic modifications. Annu Rev Biochem 2013, 82:81-118.
5. Jenuwein T., Allis C.D. Translating the histone code. Science 2001, 293:1074-1080.
6. Rando O.J. Combinatorial complexity in chromatin structure and function: revisiting the histone code. Curr Opin Genet Dev 2012, 22:148-155.
7. Chi P., Allis C.D., Wang G.G. Covalent histone modifications - miswritten, misinterpreted and mis-erased in human cancers. Nat Rev Cancer 2010, 10:457-469.
8. Greer E.L., Shi Y. Histone methylation: a dynamic mark in health, disease and inheritance. Nat Rev Genet 2012, 13:343-357.
9. Bhaumik S.R., Smith E., Shilatifard A. Covalent modifications of histones during development and disease pathogenesis. Nat Struct Mol Biol 2007, 14:1008-1016.
10. Allfrey V.G., Faulkner R., Mirsky A.E. Acetylation and methylation of histones and their possible role in the regulation of RNA synthesis. Proc Natl Acad Sci U S A 1964, 51:786-794.
11. Murray K. The occurrence of epsilon-N-methyl lysine in histones. Biochemistry 1964, 3:10-15.
12. Kouzarides T. Chromatin modifications and their function. Cell 2007, 128:693-705.
13. Park P.J. ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet 2009, 10:669-680.
14. Witze E.S., Old W.M., Resing K.A., Ahn N.G. Mapping protein post-translational modifications with mass spectrometry. Nat Methods 2007, 4:798-806.
15. Afjehi-Sadat L., Garcia B.A. Comprehending dynamic protein methylation with mass spectrometry. Curr Opin Chem Biol 2013, 17:12-19.
16. Choudhary C., Weinert B.T., Nishida Y., Verdin E., Mann M. The growing landscape of lysine acetylation links metabolism and cell signalling. Nat Rev Mol Cell Biol 2014, 15:536-550.
17. Steen H., Mann M. The ABC's (and XYZ's) of peptide sequencing. Nat Rev Mol Cell Biol 2004, 5:699-711.
18. Garcia B.A., Shabanowitz J., Hunt D.F. Characterization of histones and their post-translational modifications by mass spectrometry. Curr Opin Chem Biol 2007, 11:66-73.
19. Britton L.M., Gonzales-Cope M., Zee B.M., Garcia B.A. Breaking the histone code with quantitative mass spectrometry. Expert Rev Proteomics 2011, 8:631-643.
20. Karch K.R., Denizio J.E., Black B.E., Garcia B.A. Identification and interrogation of combinatorial histone modifications. Front Genet 2013, 4:264.
21. Arnaudo A.M., Garcia B.A. Proteomic characterization of novel histone post-translational modifications. Epigenet Chromatin 2013, 6:24.
22. Chen Y., Sprung R., Tang Y., Ball H., Sangras B., Kim S.C., Falck J.R., Peng J., Gu W., Zhao Y. Lysine propionylation and butyrylation are novel post-translational modifications in histones. Mol Cell Proteomics 2007, 6:812-819.
23. Zhang K., Chen Y., Zhang Z., Zhao Y. Identification and verification of lysine propionylation and butyrylation in yeast core histones using PTMap software. J Proteome Res 2009, 8:900-906.
24. Xie Z., Dai J., Dai L., Tan M., Cheng Z., Wu Y., Boeke J.D., Zhao Y. Lysine succinylation and lysine malonylation in histones. Mol Cell Proteomics 2012, 11:100-107.
25. Tan M., Luo H., Lee S., Jin F., Yang J.S., Montellier E., Buchou T., Cheng Z., Rousseaux S., Rajagopal N., et al. Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification. Cell 2011, 146:1016-1028.
26. Dai L., Peng C., Montellier E., Lu Z., Chen Y., Ishii H., Debernardi A., Buchou T., Rousseaux S., Jin F., et al. Lysine 2-hydroxyisobutyrylation is a widely distributed active histone mark. Nat Chem Biol 2014, 10:365-370.
27. Chen Y., Chen W., Cobb M.H., Zhao Y. PTMap - a sequence alignment software for unrestricted, accurate, and full-spectrum identification of post-translational modification sites. Proc Natl Acad Sci U S A 2009, 106:761-766.
28. Grammel M., Hang H.C. Chemical reporters for biological discovery. Nat Chem Biol 2013, 9:475-484.
29. Wilson J.P., Raghavan A.S., Yang Y.Y., Charron G., Hang H.C. Proteomic analysis of fatty-acylated proteins in mammalian cells with chemical reporters reveals S-acylation of histone H3 variants. Mol Cell Proteomics 2011, 10. M110 001198.
30. Bao X., Zhao Q., Yang T., Fung Y.M., Li X.D. A chemical probe for lysine malonylation. Angew Chem Int Ed Engl 2013, 52:4883-4886.
31. Tessarz P., Santos-Rosa H., Robson S.C., Sylvestersen K.B., Nelson C.J., Nielsen M.L., Kouzarides T. Glutamine methylation in histone H2A is an RNA-polymerase-I-dedicated modification. Nature 2014, 505:564-568.
32. Wagner G.R., Payne R.M. Widespread and enzyme-independent Nepsilon-acetylation and Nepsilon-succinylation of proteins in the chemical conditions of the mitochondrial matrix. J Biol Chem 2013, 288:29036-29045.
33. Wagner G.R., Hirschey M.D. Nonenzymatic protein acylation as a carbon stress regulated by sirtuin deacylases. Mol Cell 2014, 54:5-16.
34. Sauve A.A., Wolberger C., Schramm V.L., Boeke J.D. The biochemistry of sirtuins. Annu Rev Biochem 2006, 75:435-465.
35. Bheda P., Wang J.T., Escalante-Semerena J.C., Wolberger C. Structure of Sir2Tm bound to a propionylated peptide. Protein Sci 2011, 20:131-139.
36. Cheng Z., Tang Y., Chen Y., Kim S., Liu H., Li S.S., Gu W., Zhao Y. Molecular characterization of propionyllysines in non-histone proteins. Mol Cell Proteomics 2009, 8:45-52.
37. Peng C., Lu Z., Xie Z., Cheng Z., Chen Y., Tan M., Luo H., Zhang Y., He W., Yang K., et al. The first identification of lysine malonylation substrates and its regulatory enzyme. Mol Cell Proteomics 2011, 10. M111 012658.
38. Du J., Zhou Y., Su X., Yu J.J., Khan S., Jiang H., Kim J., Woo J., Kim J.H., Choi B.H., et al. Sirt5 is a NAD-dependent protein lysine demalonylase and desuccinylase. Science 2011, 334:806-809.
39. Jiang H., Khan S., Wang Y., Charron G., He B., Sebastian C., Du J., Kim R., Ge E., Mostoslavsky R., et al. SIRT6 regulates TNF-alpha secretion through hydrolysis of long-chain fatty acyl lysine. Nature 2013, 496:110-113.
40. Feldman J.L., Baeza J., Denu J.M. Activation of the protein deacetylase SIRT6 by long-chain fatty acids and widespread deacylation by mammalian sirtuins. J Biol Chem 2013, 288:31350-31356.
41. Jiang T., Zhou X., Taghizadeh K., Dong M., Dedon P.C. N-formylation of lysine in histone proteins as a secondary modification arising from oxidative DNA damage. Proc Natl Acad Sci U S A 2007, 104:60-65.
42. Wisniewski J.R., Zougman A., Mann M. 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 2008, 36:570-577.
43. Galligan J.J., Rose K.L., Beavers W.N., Hill S., Tallman K.A., Tansey W.P., Marnett L.J. Stable histone adduction by 4-oxo-2-nonenal: a potential link between oxidative stress and epigenetics. J Am Chem Soc 2014, 136:11864-11866.
44. Shi X., Hong T., Walter K.L., Ewalt M., Michishita E., Hung T., Carney D., Pena P., Lan F., Kaadige M.R., et al. ING2 PHD domain links histone H3 lysine 4 methylation to active gene repression. Nature 2006, 442:96-99.
45. Wysocka J., Swigut T., Xiao H., Milne T.A., Kwon S.Y., Landry J., Kauer M., Tackett A.J., Chait B.T., Badenhorst P., et al. A PHD finger of NURF couples histone H3 lysine 4 trimethylation with chromatin remodelling. Nature 2006, 442:86-90.
46. Vermeulen M., Eberl H.C., Matarese F., Marks H., Denissov S., Butter F., Lee K.K., Olsen J.V., Hyman A.A., Stunnenberg H.G., et al. Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers. Cell 2010, 142:967-980.
47. Vermeulen M., Mulder K.W., Denissov S., Pijnappel W.W., van Schaik F.M., Varier R.A., Baltissen M.P., Stunnenberg H.G., Mann M., Timmers H.T. Selective anchoring of TFIID to nucleosomes by trimethylation of histone H3 lysine 4. Cell 2007, 131:58-69.
48. Bartke T., Vermeulen M., Xhemalce B., Robson S.C., Mann M., Kouzarides T. Nucleosome-interacting proteins regulated by DNA and histone methylation. Cell 2010, 143:470-484.
49. Li X., Kapoor T.M. Approach to profile proteins that recognize post-translationally modified histone tails. J Am Chem Soc 2010, 132:2504-2505.
50. Pham N.D., Parker R.B., Kohler J.J. Photocrosslinking approaches to interactome mapping. Curr Opin Chem Biol 2013, 17:90-101.
51. Pena P.V., Davrazou F., Shi X., Walter K.L., Verkhusha V.V., Gozani O., Zhao R., Kutateladze T.G. Molecular mechanism of histone H3K4me3 recognition by plant homeodomain of ING2. Nature 2006, 442:100-103.
52. Li X., Foley E.A., Kawashima S.A., Molloy K.R., Li Y., Chait B.T., Kapoor T.M. Examining post-translational modification-mediated protein-protein interactions using a chemical proteomics approach. Protein Sci 2013, 22:287-295.
53. Li X., Foley E.A., Molloy K.R., Li Y., Chait B.T., Kapoor T.M. Quantitative chemical proteomics approach to identify post-translational modification-mediated protein-protein interactions. J Am Chem Soc 2012, 134:1982-1985.
54. Ong S.E., Blagoev B., Kratchmarova I., Kristensen D.B., Steen H., Pandey A., Mann M. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 2002, 1:376-386.
55. Su X., Zhu G., Ding X., Lee S.Y., Dou Y., Zhu B., Wu W., Li H. Molecular basis underlying histone H3 lysine-arginine methylation pattern readout by Spin/Ssty repeats of Spindlin1. Genes Dev 2014, 28:622-636.
56. Yang T., Liu Z., Li X.D. Developing diazirine-based chemical probes to identify histone modification 'readers' and 'erasers'. Chem Sci 2014, 10.1039/c4sc02328e.
57. Kalesh K.A., Tate E.W. A succinyl lysine-based photo-cross-linking peptide probe for Sirtuin 5. Org Biomol Chem 2014, 12:4310-4313.
58. Bao X., Wang Y., Li X., Li X.M., Liu Z., Yang T., Wong C.F., Zhang J., Hao Q., Li X.D. Identification of 'erasers' for lysine-crotonylated histone marks using a chemical proteomics approach. eLife 2014, 10.7554/eLife.02999.
59. Montgomery D.C., Sorum A.W., Meier J.L. Chemoproteomic profiling of lysine acetyltransferases highlights an expanded landscape of catalytic acetylation. J Am Chem Soc 2014, 136:8669-8676.
60. Nguyen U.T., Bittova L., Muller M.M., Fierz B., David Y., Houck-Loomis B., Feng V., Dann G.P., Muir T.W. Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. Nat Methods 2014, 11:834-840.
61. Fierz B., Chatterjee C., McGinty R.K., Bar-Dagan M., Raleigh D.P., Muir T.W. Histone H2B ubiquitylation disrupts local and higher-order chromatin compaction. Nat Chem Biol 2011, 7:113-119.
62. Liu B., Lin Y., Darwanto A., Song X., Xu G., Zhang K. Identification and characterization of propionylation at histone H3 lysine 23 in mammalian cells. J Biol Chem 2009, 284:32288-32295.
63. Unoki M., Masuda A., Dohmae N., Arita K., Yoshimatsu M., Iwai Y., Fukui Y., Ueda K., Hamamoto R., Shirakawa M., et al. Lysyl 5-hydroxylation, a novel histone modification, by Jumonji domain containing 6 (JMJD6). J Biol Chem 2013, 288:6053-6062.
64. Sakabe K., Wang Z., Hart G.W. Beta-N-acetylglucosamine (O-GlcNAc) is part of the histone code. Proc Natl Acad Sci U S A 2010, 107:19915-19920.
65. Fujiki R., Hashiba W., Sekine H., Yokoyama A., Chikanishi T., Ito S., Imai Y., Kim J., He H.H., Igarashi K., et al. GlcNAcylation of histone H2B facilitates its monoubiquitination. Nature 2011, 480:557-560.
66. Zhang S., Roche K., Nasheuer H.P., Lowndes N.F. Modification of histones by sugar beta-N-acetylglucosamine (GlcNAc) occurs on multiple residues, including histone H3 serine 10, and is cell cycle-regulated. J Biol Chem 2011, 286:37483-37495.
67. Tweedie-Cullen R.Y., Brunner A.M., Grossmann J., Mohanna S., Sichau D., Nanni P., Panse C., Mansuy I.M. Identification of combinatorial patterns of post-translational modifications on individual histones in the mouse brain. PLoS ONE 2012, 7:e36980.
68. Zou C., Ellis B.M., Smith R.M., Chen B.B., Zhao Y., Mallampalli R.K. Acyl-CoA:lysophosphatidylcholine acyltransferase I (Lpcat1) catalyzes histone protein O-palmitoylation to regulate mRNA synthesis. J Biol Chem 2011, 286:28019-28025.
69. Garcia-Gimenez J.L., Olaso G., Hake S.B., Bonisch C., Wiedemann S.M., Markovic J., Dasi F., Gimeno A., Perez-Quilis C., Palacios O., et al. Histone h3 glutathionylation in proliferating mammalian cells destabilizes nucleosomal structure. Antioxid Redox Signal 2013, 19:1305-1320.