Rapid immunoprecipitation mass spectrometry of endogenous proteins (RIME) for analysis of chromatin complexes

Nature Protocols

Volumn 11, Issue 2, 2016, Pages 316-326

  Mohammed, Hisham ^a,b   Taylor, Christopher ^a   Brown, Gordon D ^a   Papachristou, Evaggelia K ^a   Carroll, Jason S ^a   D'Santos, Clive S ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b BABRAHAM INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBODY; FORMALDEHYDE; CHROMATIN; PROTEIN;

CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; COMPLEX FORMATION; CONTROLLED STUDY; CROSS LINKING; IMMUNOPRECIPITATION; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; RAPID IMMUNOPRECIPITATION MASS SPECTROMETRY OF ENDOGENOUS PROTEIN; REVIEW; SEQUENCE ANALYSIS; TANDEM MASS SPECTROMETRY; CHEMISTRY; PROCEDURES; TIME FACTOR;

CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; CHROMATOGRAPHY, LIQUID; MASS SPECTROMETRY; PROTEINS; TIME FACTORS;

EID: 84961363725     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2016.020     Document Type: Review

References (57)

1. Alberts, B. The cell as a collection of protein machines: preparing the next generation of molecular biologists. Cell 92, 291-294 (1998).
2. Dunham, W.H., Mullin, M. & Gingras, A.C. Affinity-purification coupled to mass spectrometry: basic principles and strategies. Proteomics 12, 1576-1590 (2012).
3. Giambruno, R. et al. Affinity purification strategies for proteomic analysis of transcription factor complexes. J. Proteome Res. 12, 4018-4027 (2013).
4. Greenberg, R.A. et al. Multifactorial contributions to an acute DNA damage response by BRCA1/BARD1-containing complexes. Genes Dev. 20, 34-46 (2006).
5. Kocher, T. & Superti-Furga, G. Mass spectrometry-based functional proteomics: from molecular machines to protein networks. Nat. Methods 4, 807-815 (2007).
6. Marcon, E. et al. Assessment of a method to characterize antibody selectivity and specificity for use in immunoprecipitation. Nat. Methods 12, 725-731 (2015).
7. Morris, J.H. et al. Affinity purification-mass spectrometry and network analysis to understand protein-protein interactions. Nat. Protoc. 9, 2539-2554 (2014).
8. Gavin, A.C. et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141-147 (2002).
9. Ho, Y. et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415, 180-183 (2002).
10. Krogan, N.J. et al. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440, 637-643 (2006).
11. Babu, M., Krogan, N.J., Awrey, D.E., Emili, A. & Greenblatt, J.F. Systematic characterization of the protein interaction network and protein complexes in Saccharomyces cerevisiae using tandem affinity purification and mass spectrometry. Methods Mol. Biol. 548, 187-207 (2009).
12. Guruharsha, K.G. et al. A protein complex network of Drosophila melanogaster. Cell 147, 690-703 (2011).
13. Rhee, D.Y. et al. Transcription factor networks in Drosophila melanogaster. Cell Rep. 8, 2031-2043 (2014).
14. Rubio, V. et al. An alternative tandem affinity purification strategy applied to Arabidopsis protein complex isolation. Plant J. 41, 767-778 (2005).
15. Van Leene, J. et al. A tandem affinity purification-based technology platform to study the cell cycle interactome in Arabidopsis thaliana. Mol. Cell. Proteomics 6, 1226-1238 (2007).
16. Van Leene, J. et al. An improved toolbox to unravel the plant cellular machinery by tandem affinity purification of Arabidopsis protein complexes. Nat. Protoc. 10, 169-187 (2015).
17. Ogawa, H., Ishiguro, K., Gaubatz, S., Livingston, D.M. & Nakatani, Y. A complex with chromatin modifiers that occupies E2F- and Myc-responsive genes in G0 cells. Science 296, 1132-1136 (2002).
18. Ewing, R.M. et al. Large-scale mapping of human protein-protein interactions by mass spectrometry. Mol. Syst. Biol. 3, 89 (2007).
19. Sowa, M.E., Bennett, E.J., Gygi, S.P. & Harper, J.W. Defining the human deubiquitinating enzyme interaction landscape. Cell 138, 389-403 (2009).
20. Zhou, Z., Licklider, L.J., Gygi, S.P. & Reed, R. Comprehensive proteomic analysis of the human spliceosome. Nature 419, 182-185 (2002).
21. Huttlin, E.L. et al. The BioPlex network: a systematic exploration of the human interactome. Cell 162, 425-440 (2015).
22. Tsai, A. & Carstens, R.P. An optimized protocol for protein purification in cultured mammalian cells using a tandem affinity purification approach. Nat. Protoc. 1, 2820-2827 (2006).
23. Malovannaya, A. et al. Analysis of the human endogenous coregulator complexome. Cell 145, 787-799 (2011).
24. Malovannaya, A. et al. Streamlined analysis schema for high-throughput identification of endogenous protein complexes. Proc. Natl. Acad. Sci. USA 107, 2431-2436 (2010).
25. Brohee, S., Faust, K., Lima-Mendez, G., Vanderstocken, G. & van Helden, J. Network analysis tools: from biological networks to clusters and pathways. Nat. Protoc. 3, 1616-1629 (2008).
26. Bensimon, A., Heck, A.J. & Aebersold, R. Mass spectrometry-based proteomics and network biology. Annu. Rev. Biochem. 81, 379-405 (2012).
27. Drewes, G. & Bouwmeester, T. Global approaches to protein-protein interactions. Curr. Opin. Cell Biol. 15, 199-205 (2003).
28. Kutzera, J. et al. Inferring protein-protein interaction complexes from immunoprecipitation data. BMC Res. Notes 6, 468 (2013).
29. Chiang, T. & Scholtens, D. A general pipeline for quality and statistical assessment of protein interaction data using R and Bioconductor. Nat. Protoc. 4, 535-546 (2009).
30. Selbach, M. & Mann, M. Protein interaction screening by quantitative immunoprecipitation combined with knockdown (QUICK). Nat. Methods 3, 981-983 (2006).
31. Trinkle-Mulcahy, L. Resolving protein interactions and complexes by affinity purification followed by label-based quantitative mass spectrometry. Proteomics 12, 1623-1638 (2012).
32. Trinkle-Mulcahy, L. et al. Identifying specific protein interaction partners using quantitative mass spectrometry and bead proteomes. J. Cell Biol. 183, 223-239 (2008).
33. Tackett, A.J. et al. I-DIRT, a general method for distinguishing between specific and nonspecific protein interactions. J. Proteome Res. 4, 1752-1756 (2005).
34. Mellacheruvu, D. et al. The CRAPome: a contaminant repository for affinity purification-mass spectrometry data. Nat. Methods 10, 730-736 (2013).
35. Mohammed, H. et al. Endogenous purification reveals GREB1 as a key estrogen receptor regulatory factor. Cell Rep. 3, 342-349 (2013).
36. Mohammed, H. et al. Progesterone receptor modulates ER action in breast cancer. Nature 523, 313-317 (2015).
37. Srinivasa, S., Ding, X. & Kast, J. Formaldehyde cross-linking and structural proteomics: bridging the gap. Methods 89, 91-98 (2015).
38. Sutherland, B.W., Toews, J. & Kast, J. Utility of formaldehyde cross-linking and mass spectrometry in the study of protein-protein interactions. J. Mass Spectrom. 43, 699-715 (2008).
39. Vasilescu, J., Guo, X. & Kast, J. Identification of protein-protein interactions using in vivo cross-linking and mass spectrometry. Proteomics 4, 3845-3854 (2004).
40. Ramos-Vara, J.A. Principles and methods of immunohistochemistry. Methods Mol. Biol. 691, 83-96 (2011).
41. Schmidt, D. et al. ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Methods 48, 240-248 (2009).
42. Latos, P.A. et al. Fgf and Esrrb integrate epigenetic and transcriptional networks that regulate self-renewal of trophoblast stem cells. Nat. Commun. 6, 7776 (2015).
43. Xu, Y. et al. LMTK3 represses tumor suppressor-like genes through chromatin remodeling in breast cancer. Cell Rep. 12, 837-849 (2015).
44. Sanders, D.A. et al. FOXM1 binds directly to non-consensus sequences in the human genome. Genome Biol. 16, 130 (2015).
45. Ji, Z. et al. The forkhead transcription factor FOXK2 acts as a chromatin targeting factor for the BAP1-containing histone deubiquitinase complex. Nucleic Acids Res. 42, 6232-6242 (2014).
46. Ali, S. & Coombes, R.C. Endocrine-responsive breast cancer and strategies for combating resistance. Nat. Rev. Cancer 2, 101-112 (2002).
47. Metivier, R. et al. Estrogen receptor- directs ordered, cyclical, and combinatorial recruitment of cofactors on a natural target promoter. Cell 115, 751-763 (2003).
48. Okada, M. et al. Switching of chromatin-remodelling complexes for oestrogen receptor-α. EMBO Rep. 9, 563-568 (2008).
49. Metz, B. et al. Identification of formaldehyde-induced modifications in proteins: reactions with insulin. Bioconjug. Chem. 17, 815-822 (2006).
50. Metz, B. et al. Identification of formaldehyde-induced modifications in proteins: reactions with model peptides. J. Biol. Chem. 279, 6235-6243 (2004).
51. Byrum, S.D., Raman, A., Taverna, S.D. & Tackett, A.J. ChAP-MS: a method for identification of proteins and histone posttranslational modifications at a single genomic locus. Cell Rep. 2, 198-205 (2012).
52. Pourfarzad, F. et al. Locus-specific proteomics by TChP: targeted chromatin purification. Cell Rep. 4, 589-600 (2013).
53. Soldi, M. & Bonaldi, T. The ChroP approach combines ChIP and mass spectrometry to dissect locus-specific proteomic landscapes of chromatin. J. Vis. Exp. (2014).
54. Wang, C.I. et al. Chromatin proteins captured by ChIP-mass spectrometry are linked to dosage compensation in Drosophila. Nat. Struct. Mol. Biol. 20, 202-209 (2013).
55. Engelen, E. et al. Proteins that bind regulatory regions identified by histone modification chromatin immunoprecipitations and mass spectrometry. Nat. Commun. 6, 7155 (2015).
56. Ji, X. et al. Chromatin proteomic profiling reveals novel proteins associated with histone-marked genomic regions. Proc. Natl. Acad. Sci. USA 112, 3841-3846 (2015).
57. Boyer, L.A. et al. Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122, 947-956 (2005).