Quantification of histone modifications using 15N metabolic labeling

Methods

Volumn 61, Issue 3, 2013, Pages 236-243

  Zhang, Chunchao ^a   Liu, Yifan ^a   Andrews, Philip C ^a,b  

^a UNIVERSITY OF MICHIGAN   (United States)

^b UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

Author keywords

15N metabolic labeling; Histone; Mass spectrometry; Post translational modification

Indexed keywords

HISTONE ACETYLTRANSFERASE; METHYLTRANSFERASE; NITROGEN 15; STABLE ISOTOPE;

ARTICLE; CELL CULTURE; EMBRYONIC STEM CELL; HISTONE ACETYLATION; HISTONE MODIFICATION; HUMAN; HYDROPHILIC INTERACTION CHROMATOGRAPHY; HYDROPHOBICITY; ION PAIR CHROMATOGRAPHY; ISOTOPE LABELING; LIQUID CHROMATOGRAPHY; NONHUMAN; PRIORITY JOURNAL; PROTEIN PHOSPHORYLATION; PROTEOMICS; QUANTITATIVE ANALYSIS; REVERSED PHASE HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; TANDEM MASS SPECTROMETRY; TETRAHYMENA THERMOPHILA;

ACETYLATION; AMINO ACID SEQUENCE; ESCHERICHIA COLI; GENE EXPRESSION; HISTONES; HUMANS; ISOTOPE LABELING; MASS SPECTROMETRY; METHYLATION; MOLECULAR SEQUENCE DATA; NITROGEN ISOTOPES; PEPTIDES; PROTEIN PROCESSING, POST-TRANSLATIONAL; RECOMBINANT PROTEINS; TETRAHYMENA THERMOPHILA;

TETRAHYMENA THERMOPHILA;

EID: 84879573913     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2013.02.004     Document Type: Article

References (59)

1. Aebersold R., Mann M. Nature 2003, 422:198-207.
2. Cox J., Mann M. Annu. Rev. Biochem. 2011, 80:273-299.
3. Schulze W.X., Usadel B. Annu. Rev. Plant Biol. 2010, 61:491-516.
4. Ong S.-E., Mann M. Nat. Chem. Biol. 2005, 1:252-262.
5. Kirkpatrick D.S., Gerber S.A., Gygi S.P. Methods 2005, 35:265-273.
6. Xie F., Liu T., Qian W.-J. J. Biol. Chem. 2011, 286:25443-25449.
7. Anderson L., Hunter C.L. Mol. Cell. Proteomics 2006, 5:573-588.
8. Carr S.A., Anderson L. Clin. Chem. 2008, 54:1749-1752.
9. Pan S., Aebersold R., Chen R., Rush J., Goodlett D.R., Mcintosh M.W., Zhang J., Brentnall T.A. J. Proteome Res. 2009, 8:787-797.
10. Zhu W., Smith J.W., Huang C.-M. J. Biomed. Biotechnol. 2010, 2010:840518.
11. Wang M., You J., Bemis K.G., Tegeler T.J., Brown D.P.G. Brief. Funct. Genomic. Proteomic. 2008, 7:329-339.
12. Sidoli S., Cheng L., Jensen O.N. J. Proteomics 2012, 75:3419-3433.
13. Britton L.-M.P., Gonzales-Cope M., Zee B.M., Garcia B.A. Expert Rev. Proteomics 2011, 8:631-643.
14. Neilson K.A., Ali N.A., Muralidharan S., Mirzaei M., Mariani M., Assadourian G., Lee A., van Sluyter S.C., Haynes P.A. Proteomics 2011, 11:533-535.
15. Old W.M., Meyer-Arendt K., Aveline-Wolf L., Pierce K.G., Mendoza A., Sevinsky J.R. Mol. Cell. Proteomics 2005, 4:1487-1502.
16. Steen H., Jebanathirajah J.A., Springer M., Kirschner M.W. Proc. Natl. Acad. Sci. USA 2005, 102:3948-3953.
17. Beck H.C., Nielsen E.C., Matthiesen R., Jensen L.H., Sehested M., Finn P., Grauslund M., Hansen A.M., Jensen O.N. Mol. Cell. Proteomics 2006, 5:1314-1325.
18. Drogaris P., Villeneuve V., Pomiès C., Lee E.-H., Bourdeau V., Bonneil E., Ferbeyre G., Verreault A., Thibault P. Sci. Rep. 2012, 2:220.
19. Drogaris P., Wurtele H., Masumoto H., Verreault A., Thibault P. Anal. Chem. 2008, 80:6698-6707.
20. Phanstiel D., Brumbaugh J., Berggren W.T., Conard K., Feng X., Levenstein M.E., McAlister G.C. Proc. Natl. Acad. Sci. USA 2008, 105:4093-4098.
21. Beynon R.J., Pratt J.M. Mol. Cell. Proteomics 2005, 4:857-872.
22. Bantscheff M., Schirle M., Sweetman G., Rick J., Kuster B. Anal. Bioanal. Chem. 2007, 389:1017-1031.
23. Oda Y., Huang K., Cross F.R., Cowburn D., Chait B.T. Proc. Natl. Acad. Sci. USA 1999, 96:6591-6596.
24. Ong S.-E. Mol. Cell. Proteomics 2002, 1:376-386.
25. Jung H.R., Pasini D., Helin K., Jensen O.N. Mol. Cell. Proteomics 2010, 9:838-850.
26. Cuomo A., Moretti S., Minucci S., Bonaldi T. Amino Acids 2011, 41:387-399.
27. Plazas-Mayorca M.D., Zee B.M., Young N.L., Fingerman I.M., LeRoy G., Briggs S.D. J. Proteome Res. 2009, 8:5367-5374.
28. Plazas-Mayorca M.D., Bloom J.S., Zeissler U., Leroy G., Young N.L., DiMaggio P.A., Krugylak L., Schneider R., Garcia B.A. Mol. Biosyst. 2010, 6:1719-1729.
29. Garcia B.A., Mollah S., Ueberheide B.M. Nat. Protoc. 2007, 2:933-938.
30. Young N.L., DiMaggio P.A., Plazas-Mayorca M.D., Baliban R.C., Floudas C.A., Garcia B.A. Mol. Cell. Proteomics 2009, 8:2266-2284.
31. Boersema P.J., Mohammed S., Heck A.J.R. Anal. Bioanal. Chem. 2008, 391:151-159.
32. Arnaudo A.M., Molden R.C. Crit. Rev. Biochem. Mol. Biol. 2011, 46:284-294.
33. Eberl H.C., Mann M., Vermeulen M. Chembiochem 2011, 12:224-234.
34. Gouw J.W., Krijgsveld J., Heck A.J.R. Mol. Cell. Proteomics 2010, 9:11-24.
35. Ishihama Y., Sato T., Tabata T., Miyamoto N., Sagane K., Nagasu T., Oda Y. Nat Biotech. 2005, 23:617-621.
36. Mcclatchy D.B., Dong M.-qiu, Wu C.C., Venable J.D., Yates J.R. 15N metabolic labeling of mammalian tissue with slow protein turnover. J. Proteome Res. 2007, 6:2005-2010.
37. Wu C.C., MacCoss M.J., Howell K.E., Matthews D.E., Yates J.R. Anal. Chem. 2004, 76:4951-4959.
38. Krijgsveld J., Ketting R.F., Mahmoudi T., Johansen J., Artal-sanz M., Verrijzer C.P., Plasterk R.H.A., Heck A.J.R. Nat. Biotech. 2003, 21:927-931.
39. Engelsberger W.R., Erban A., Kopka J., Schulze W.X. Plant Methods 2006, 2:14.
40. Lanquar V., Kuhn L., Lelièvre F., Khafif M., Espagne C., Bruley C., Barbier-Brygoo H., Garin J., Thomine S. Proteomics 2007, 7:750-754.
41. Orias E. Genome Res. 1998, 8:91-99.
42. Gorovsky M.A. J. Cell Biol. 1970, 47:619-630.
43. Gorovsky M.A. J. Cell Biol. 1970, 47:631-636.
44. Kouzarides T. Cell 2007, 128:693-705.
45. Zhang K., Chen Y., Zhang Z., Zhao Y. J. Proteome Res. 2009, 8:900-906.
46. Tan M., Luo H., Lee S., Jin F., Yang J.S., Montellier E., Buchou T., Cheng Z., Rousseaux S., Rajagopal N., Lu Z., Ye Z., Zhu Q., Wysocka J., Ye Y., Khochbin S., Ren B., Zhao Y. Cell 2011, 146:1016-1028.
47. Zhang Z., Tan M., Xie Z., Dai L., Chen Y., Zhao Y. Nat. Chem. Biol. 2010, 7:58-63.
48. Krebs J.E. Mol. Biosyst. 2007, 3:8-12.
49. Zee B.M., Levin R.S., Xu B., LeRoy G., Wingreen N.S. J. Biol. Chem. 2010, 285:3341-3350.
50. Su X., Ren C., Freitas M.A. Expert Rev. Proteomics 2007, 4:211-225.
51. Ueberheide B., Mollah S. Int. J. Mass Spectrom. 2007, 259:46-56.
52. Zhang K., Tang H. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 2003, 783:173-179.
53. Garcia B.A., Shabanowitz J., Hunt D.F. Curr. Opin. Chem. Biol. 2007, 11:66-73.
54. C. Zhang, A.J. Molascon, S. Gao, Y. Liu, P.C. Andrews, Quantitative proteomics reveals that the specific methyltransferases Txr1p and Ezl2p differentially affect the mono-, di- and tri-methylation states of histone H3 lysine 27. Mol. Cell. Proteomics, in press, PMID: 23150054.
55. Rea S., Eisenhaber F., O'Carroll D., Strahl B.D., Sun Z.W., Schmid M., Opravil S., Mechtler K., Ponting C.P., Allis C.D., Jenuwein T. Nature 2000, 406:593-599.
56. Mosammaparast N., Shi Y. Annu. Rev. Biochem. 2010, 79:155-179.
57. Zhang K., Dent S.Y.R. J. Cell. Biochem. 2005, 1148:1137-1148.
58. Czermin B., Melfi R., McCabe D., Seitz V., Imhof A., Pirrotta V. Cell 2002, 111:185-196.
59. Jacob Y., Feng S. Nat. Struct. Mol. Biol. 2009, 16:763-768.