Table of Contents
International Journal of Proteomics
Volume 2012, Article ID 630409, 12 pages
http://dx.doi.org/10.1155/2012/630409
Research Article

Chromatin-Associated Proteins Revealed by SILAC-Proteomic Analysis Exhibit a High Likelihood of Requirement for Growth Fitness under DNA Damage Stress

1School of Biological Science, Nanyang Technological University, Singapore 637551
2Systems Biology, Genome Institute of Singapore, Singapore 138672
3Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077

Received 11 February 2012; Accepted 9 June 2012

Academic Editor: Winston Patrick Kuo

Copyright © 2012 Han Wang et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. K. E. Van Hoide, C. G. Sahasrabuddhe, and B. R. Shaw, “A model for particulate structure in chromatin,” Nucleic Acids Research, vol. 1, no. 11, pp. 1579–1586, 1974. View at Publisher · View at Google Scholar · View at Scopus
  2. K. Luger, A. W. Mäder, R. K. Richmond, D. F. Sargent, and T. J. Richmond, “Crystal structure of the nucleosome core particle at 2.8 Å resolution,” Nature, vol. 389, no. 6648, pp. 251–260, 1997. View at Publisher · View at Google Scholar · View at Scopus
  3. B. D. Strahl and C. D. Allis, “The language of covalent histone modifications,” Nature, vol. 403, no. 6765, pp. 41–45, 2000. View at Publisher · View at Google Scholar · View at Scopus
  4. E. Bernstein and C. D. Allis, “RNA meets chromatin,” Genes and Development, vol. 19, no. 14, pp. 1635–1655, 2005. View at Publisher · View at Google Scholar · View at Scopus
  5. M. Bühler and D. Moazed, “Transcription and RNAi in heterochromatic gene silencing,” Nature Structural and Molecular Biology, vol. 14, no. 11, pp. 1041–1048, 2007. View at Publisher · View at Google Scholar · View at Scopus
  6. A. J. Link, J. Eng, D. M. Schieltz et al., “Direct analysis of protein complexes using mass spectrometry,” Nature Biotechnology, vol. 17, no. 7, pp. 676–682, 1999. View at Publisher · View at Google Scholar · View at Scopus
  7. M. Brajenovic, G. Joberty, B. Küster, T. Bouwmeester, and G. Drewes, “Comprehensive proteomic analysis of human par protein complexes reveals an interconnected protein network,” Journal of Biological Chemistry, vol. 279, no. 13, pp. 12804–12811, 2004. View at Publisher · View at Google Scholar · View at Scopus
  8. R. M. Ewing, P. Chu, F. Elisma et al., “Large-scale mapping of human protein-protein interactions by mass spectrometry,” Molecular Systems Biology, vol. 3, article 89, 2007. View at Publisher · View at Google Scholar · View at Scopus
  9. A. C. Gavin, P. Aloy, P. Grandi et al., “Proteome survey reveals modularity of the yeast cell machinery,” Nature, vol. 440, no. 7084, pp. 631–636, 2006. View at Publisher · View at Google Scholar · View at Scopus
  10. Y. Ho, A. Gruhler, A. Heilbut et al., “Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry,” Nature, vol. 415, no. 6868, pp. 180–183, 2002. View at Publisher · View at Google Scholar · View at Scopus
  11. N. J. Krogan, G. Cagney, H. Yu et al., “Global landscape of protein complexes in the yeast Saccharomyces cerevisiae,” Nature, vol. 440, no. 7084, pp. 637–643, 2006. View at Publisher · View at Google Scholar · View at Scopus
  12. E. H. Bayne, S. A. White, A. Kagansky et al., “Stc1: a critical link between RNAi and chromatin modification required for heterochromatin integrity,” Cell, vol. 140, no. 5, pp. 666–677, 2010. View at Publisher · View at Google Scholar · View at Scopus
  13. D. Griffiths, M. Uchiyama, P. Nurse, and T. S. F. Wang, “A novel mutant allele of the chromatin-bound fission yeast checkpoint protein Rad17 separates the DNA structure checkpoints,” Journal of Cell Science, vol. 113, part 6, pp. 1075–1088, 2000. View at Google Scholar · View at Scopus
  14. Z. Lygerou and P. Nurse, “The fission yeast origin recognition complex is constitutively associated with chromatin and is differentially modified through the cell cycle,” Journal of Cell Science, vol. 112, no. 21, pp. 3703–3712, 1999. View at Google Scholar · View at Scopus
  15. D. Hermand and P. Nurse, “Cdc18 enforces long-term maintenance of the S phase checkpoint by anchoring the Rad3-Rad26 complex to chromatin,” Molecular Cell, vol. 26, no. 4, pp. 553–563, 2007. View at Publisher · View at Google Scholar · View at Scopus
  16. S. P. Selvanathan, A. G. Thakurta, J. Dhakshnamoorthy, M. Zhou, T. D. Veenstra, and R. Dhar, “Schizosaccharomyces pombe Dss1p Is a DNA damage checkpoint protein that recruits Rad24p, Cdc25p, and Rae1p to DNA double-strand breaks,” Journal of Biological Chemistry, vol. 285, no. 19, pp. 14122–14133, 2010. View at Publisher · View at Google Scholar · View at Scopus
  17. S. E. Ong, B. Blagoev, I. Kratchmarova et al., “Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics,” Molecular & Cellular Proteomics, vol. 1, no. 5, pp. 376–386, 2002. View at Google Scholar · View at Scopus
  18. C. C. Bicho, F. D. L. Alves, Z. A. Chen, J. Rappsilber, and K. E. Sawin, “A genetic engineering solution to the “arginine conversion problem” in stable isotope labeling by amino acids in cell culture (SILAC),” Molecular and Cellular Proteomics, vol. 9, no. 7, pp. 1567–1577, 2010. View at Publisher · View at Google Scholar · View at Scopus
  19. A. Matsuyama, R. Arai, Y. Yashiroda et al., “ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe,” Nature Biotechnology, vol. 24, no. 7, pp. 841–847, 2006. View at Publisher · View at Google Scholar · View at Scopus
  20. P. J. Horn, J. N. Bastie, and C. L. Peterson, “A Rik1-associated, cullin-dependent E3 ubiquitin ligase is essential for heterochromatin formation,” Genes and Development, vol. 19, no. 14, pp. 1705–1714, 2005. View at Publisher · View at Google Scholar · View at Scopus
  21. A. Roguev, S. Bandyopadhyay, M. Zofall et al., “Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast,” Science, vol. 322, no. 5900, pp. 405–410, 2008. View at Publisher · View at Google Scholar · View at Scopus
  22. A. Roguev, A. Shevchenkon, D. Schaft, H. Thomas, A. F. Stewart, and A. Shevchenko, “A comparative analysis of an orthologous proteomic environment in the yeast Saccharomyces cerevisiae and Schizosaccharomyces pombe,” Molecular and Cellular Proteomics, vol. 3, no. 2, pp. 125–132, 2004. View at Publisher · View at Google Scholar · View at Scopus
  23. S. A. Lacadie and M. Rosbash, “Cotranscriptional spliceosome assembly dynamics and the role of U1 snRNA:5′ss base pairing in yeast,” Molecular Cell, vol. 19, no. 1, pp. 65–75, 2005. View at Publisher · View at Google Scholar · View at Scopus
  24. M. Eshaghi, J. H. Lee, L. Zhu et al., “Genomic binding profiling of the fission yeast stress-activated MAPK sty1 and the bZIP transcriptional activator Atf1 in response to H2O2,” PLoS ONE, vol. 5, no. 7, Article ID e11620, 2010. View at Publisher · View at Google Scholar · View at Scopus
  25. J. P. Lambert, L. Mitchell, A. Rudner, K. Baetz, and D. Figeys, “A novel proteomics approach for the discovery of chromatin-associated protein networks,” Molecular & Cellular Proteomics, vol. 8, no. 4, pp. 870–882, 2009. View at Publisher · View at Google Scholar · View at Scopus
  26. A. Bimbó, Y. Jia, L. P. Siew et al., “Systematic deletion analysis of fission yeast protein kinases,” Eukaryotic Cell, vol. 4, no. 4, pp. 799–813, 2005. View at Publisher · View at Google Scholar · View at Scopus
  27. J. K. Eng, A. L. McCormack, and J. R. Yates, “An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database,” Journal of the American Society for Mass Spectrometry, vol. 5, no. 11, pp. 976–989, 1994. View at Google Scholar · View at Scopus
  28. A. Keller, A. I. Nesvizhskii, E. Kolker, and R. Aebersold, “Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search,” Analytical Chemistry, vol. 74, no. 20, pp. 5383–5392, 2002. View at Publisher · View at Google Scholar · View at Scopus
  29. D. K. Han, J. Eng, H. Zhou, and R. Aebersold, “Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry,” Nature Biotechnology, vol. 19, no. 10, pp. 946–951, 2001. View at Publisher · View at Google Scholar · View at Scopus