Exploring DNA-binding proteins with in vivo chemical cross-linking and mass spectrometry

Journal of Proteome Research

Volumn 8, Issue 4, 2009, Pages 1983-1991

  Qiu, Haibo ^a   Wang, Yinsheng ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Chemical cross linking; DNA repair; DNA binding protein; Formaldehyde; Mass spectrometry; Transcription factors

Indexed keywords

DNA; DNA BINDING PROTEIN; FORMALDEHYDE; NUCLEIC ACID BINDING PROTEIN;

ARTICLE; CONTROLLED STUDY; CROSS LINKING; DNA PROTEIN COMPLEX; DNA REPAIR; DNA REPLICATION; DNA TRANSCRIPTION; GENE CONTROL; HUMAN; HUMAN CELL; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN PURIFICATION;

CELL LINE, TUMOR; CHROMATOGRAPHY, LIQUID; CROSS-LINKING REAGENTS; DNA-BINDING PROTEINS; FORMALDEHYDE; HUMANS; PROTEOME; TANDEM MASS SPECTROMETRY;

EID: 65249139434     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr8009319     Document Type: Article

References (48)

1. Carey, M.; Smale, S. T. Transcriptional regulation in eukaryotes: concepts, strategies, and techniques; Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY, 2000.
2. Levine, M.; Tjian, R. Transcription regulation and animal diversity. Nature 2003, 424, 147-151.
3. Naar, A. M.; Lemon, B. D.; Tjian, R. Transcriptional coactivator complexes. Annu. Rev. Biochem. 2001, 70, 475-501.
4. Garner, M. M.; Revzin, A. The use of gel-electrophoresis to detect and study nucleic-acid protein interactions. Trends Biochem. Sci. 1986, 11, 395-396.
5. Fried, M. G. Measurement of protein-DNA interaction parameters by electrophoresis mobility shift assay. Electrophoresis 1989, 10, 366-376.
6. Hellman, L. M.; Fried, M. G. Electrophoretic mobility shift assay (EMSA) for detecting protein-nucleic acid interactions. Nat. Protoc. 2007, 2, 1849-1861.
7. Chen, H. W.; Lin, R. J.; Xie, W.; Wilpitz, D.; Evans, R. M. Regulation of hormone-induced histone hyperacetylation and gene activation via acetylation of an acetylase. Cell 1999, 98, 675-686.
8. Spencer, V. A.; Sun, J. M.; Li, L.; Davie, J. R. Chromatin immuno-precipitation: a tool for studying histone acetylation and transcription factor binding. Methods 2003, 31, 67-75.
9. Kuo, M. H.; Allis, C. D. In vivo cross-linking and immunoprecipi-tation for studying dynamic Protein:DNA associations in a chromatin environment. Methods 1999, 19, 425-433.
10. Orlando, V. Mapping chromosomal proteins in vivo by formalde-hyde- crosslinked-chromatin immunoprecipitation. Trends Biochem. Sci. 2000, 25, 99-104.
11. Ahn, N. G.; Shabb, J. B.; Old, W. M.; Resing, K. A. Achieving indepth proteomics profiling by mass spectrometry. ACS Chem. Biol. 2007, 2, 39-52.
12. Cravatt, B. F.; Simon, G. M.; Yates, J. R. The biological impact of mass-spectrometry-based proteomics. Nature2007, 450, 991-1000.
13. Nordhoff, E.; Lehrach, H. Identification and characterization of DNA-binding proteins by mass spectrometry. Adv. Biochem. Eng. Biotechnol. 2007, 104, 111-195.
14. Barthelery, M.; Salli, U.; Vrana, K. E. Nuclear proteomics and directed differentiation of embryonic stem cells. Stem Cells Dev. 2007, 16, 905-919.
15. Barthelery, M.; Salli, U.; Vrana, K. E. Enhanced nuclear proteomics. Proteomics 2008, 8, 1832-1838.
16. Escobar, M. A.; Hoelz, D. J.; Sandoval, J. A.; Hickey, R. J.; Grosfeld, J. L.; Malkas, L. H. Profiling of nuclear extract proteins from human neuroblastoma cell lines: the search for fingerprints. J. Pediatr. Sure. 2005, 40, 349-358.
17. Jung, E.; Hoogland, C.; Chiappe, D.; Sanchez, J. C.; Hochstrasser, D. F. The establishment of a human liver nuclei two-dimensional lectrophoresis reference map. Electrophoresis 2000, 21, 3483-3487.
18. almstrom, J.; Larsen, K.; Malmstrom, L.; Tufvesson, E.; Parker,; Marchese, J.; Williamson, B.; Patterson, D.; Martin, S.; Juhasz, P.; Westergren-Thorsson, G.; Marko-Varga, G. Nanocapillary liquid chromatography interfaced to tandem matrix-assisted laser de-sorption/ionization and electrospray ionization-mass spectrometry: Mapping the nuclear proteome of human fibroblasts. Electrophoresis 2003, 24, 3806-3814.
19. Tan, F.; Li, G. S.; Chitteti, B. R.; Peng, Z. H. Proteome and phosphoproteome analysis of chromatin associated proteins in rice (Oryza sativa). Proteomics 2007, 7, 4511-4527.
20. Andersen, J. S.; Lam, Y. W.; Leung, A. K. L.; Ong, S. E.; Lyon, C. E.; Lamond, A. I.; Mann, M. Nucleolar proteome dynamics. Nature 2005, 433, 77-83.
21. Andersen, J. S.; Lyon, C. E.; Fox, A. H.; Leung, A. K. L.; Lam, Y. W.; Steen, H.; Mann, M.; Lamond, A. I. Directed proteomic analysis of the human nucleolus. Curr. Biol. 2002, 12, 1-11.
22. Coute, Y.; Burgess, J. A.; Diaz, J. J.; Chichester, C.; Lisacek, F.; Greco, A.; Sanchez, J. C. Deciphering the human nucleolar proteome. Mass Spectrom. Rev. 2006, 25, 215-234.
23. Hinsby, A. M.; Kiemer, L.; Karlberg, E. O.; Lage, K.; Fausboll, A.; Juncker, A. S.; Andersen, J. S.; Mann, M.; Brunak, S. A wiring of the human nucleolus. Mol. Cell 2006, 22, 285-295.
24. Scherl, A.; Coute, Y.; Deon, C.; Calle, A.; Kindbeiter, K.; Sanchez, J. C.; Greco, A.; Hochstrasser, D.; Diaz, J. J. Functional proteomic analysis of human nucleolus. Mol. Biol. Cell 2002, 13, 4100-4109.
25. Henrich, S.; Cordwell, S. J.; Crossett, B.; Baker, M. S.; Christopherson, R. I. The nuclear proteome and DNA-binding fraction of human Raji lymphoma cells. Biochim. Biophys. Acta, Proteins Proteomics 2007, 1774, 413-432.
26. Afjehi-Sadat, L.; Engidawork, E.; Slavc, I.; Lubec, G. Comparative proteomic analysis of nucleic acid-binding proteins in ten human tumor cell lines. Int. J. Oncol. 2006, 28, 173-190.
27. Vigneault, F.; Guerin, S. L. Regulation of gene expression: probing DNA-protein interactions in vivo and in vitro. Expert Rev. Proteomics 2005, 2, 705-718.
28. Jackson, V. Formaldehyde cross-linking for studying nucleosomal dynamics. Methods 1999, 17, 125-139.
29. Orlando, V.; Strutt, H.; Paro, R. Analysis of chromatin structure by in vivo formaldehyde cross-linking. Methods 1997, 11, 205-214.
30. Guerrero, C.; Tagwerker, C.; Kaiser, P.; Huang, L. An integrated mass spectrometry-based proteomic approach - Quantitative analysis of tandem affinity-purified in vivo cross-linked protein complexes (QTAX) to decipher the 26 S proteasome-interacting network. Mol. Cell. Proteomics 2006, 5, 366-378.
31. Vasilescu, J.; Guo, X. C.; Kast, J. Identification of protein-protein interactions using in vivo cross-linking and mass spectrometry. Proteomics 2004, 4, 3845-3854.
32. Metz, B.; Kersten, G. F. A.; Hoogerhout, P.; Brugghe, H. F.; Timmermans, H. A. M.; de Jong, A.; Meiring, H.; ten Hove, J.; Hennink, W. E.; Crommelin, D. J. A.; Jiskoot, W. Identification of formaldehyde-induced modifications in proteins - Reactions with model peptides. J. Biol. Chem. 2004, 279, 6235-6243.
33. Solomon, M. J.; Varshavsky, A. Formaldehyde-mediated DNA protein crosslinking - a probe for in vivo chromatin structures. Proc. Natl. Acad. Sci. U.S.A. 1985, 82, 6470-6474.
34. Barker, S.; Murray, D.; Zheng, J.; Li, L.; Weinfeld, M. A method for the isolation of covalent DNA-protein crosslinks suitable for proteomics analysis. Anal. Biochem. 2005, 344, 204-215.
35. Barker, S.; Weinfeld, M.; Zheng, J.; Li, L.; Murray, D. Identification of mammalian proteins cross-linked to DNA by ionizing radiation. J. Biol. Chem. 2005, 280, 33826-33838.
36. Sambrook, J.; Russell, D. W. Molecular Cloning: A Laboratory Manual, 3rd ed.; Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY, 2001.
37. McCarthy, F. M.; Bridges, S. M.; Wang, N.; Magee, G. B.; Williams, W. P.; Luthe, D. S.; Burgess, S. C. AgBase: a unified resource for functional analysis in agriculture. Nucleic Acids Res. 2007, 35, D599-D603.
38. Reardon, J. T.; Cheng, Y.; Sancar, A. Repair of DNA-protein crosslinks in mammalian cells. Cell Cycle 2006, 5, 1366-1370.
39. Nordhoff, E.; Krogsdam, A. M.; Jorgensen, H. F.; Kallipolitis, B. H.; Clark, B. F. C.; Roepstorff, P.; Kristiansen, K. Rapid identification of DNA-binding proteins by mass spectrometry. Nat. Biotechnol. 1999, 17, 884-888.
40. Yaneva, M.; Tempst, P. Affinity capture of specific DNA-binding proteins for mass spectrometric identification. Anal. Chem. 2003, 75, 6437-6448.
41. Yan, H.; Gibson, S.; Tye, B. K. Mcm2 and Mcm3, 2 proteins important for Ars activity, are related in structure and function. Genes Dev. 1991, 5, 944-957.
42. Ramnath, N.; Hernandez, F. J.; Tan, D. F.; Huberman, J. A.; Natarajan, N.; Beck, A. F.; Hyland, A.; Todorov, I. T.; Brooks, J. S. J.; Bepler, G. MCM2 is an independent predictor of survival in patients with non-small-cell lung cancer. J. Clin. Oncol. 2001, 19, 4259-4266.
43. Valkov, N. I.; Ivanova, M. I.; Uscheva, A. A.; Krachmarov, C. P. Association of Actin with DNA and nuclear matrix from guerin ascites tumor cells. Mol. Cell. Biochem. 1989, 87, 47-56.
44. Nakayasu, H.; Yoshimura, Y.; Ueda, K. Association of Actin-filaments with the nuclear matrix from bovine lymphocytes. Cell Struct. Funct. 1981, 6, 424-424.
45. Verheijen, R.; Vanvenrooij, W.; Ramaekers, F. The nuclear matrix - structure and composition. J. Cell Sci. 1988, 90, 11-36.
46. Fuentes, M.; Segura, R. L.; Abian, O.; Betancor, L.; Hidalgo, A.; Mateo, C.; Fernandez-Lafuente, R.; Guisan, J. M. Determination of protein-protein interactions through aldehyde-dextran inter-molecular cross-linking. Proteomics 2004, 4, 2602-2607.
47. Fuentes, M.; Mateo, C.; Pessela, B. C. C.; Guisan, J. M.; Fernandez-Lafuente, R. Purification, stabilization, and concentration of very weak protein-protein complexes: Shifting the association equilibrium via complex selective adsorption on lowly activated supports. Proteomics 2005, 5, 4062-4069.
48. Chong, J. P. J.; Mahbubani, H. M.; Khoo, C. Y.; Blow, J. J. Purification of an Mcm-containing complexes a component of the DNA-replication licensing system. Nature 1995, 375, 418-421.