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Volumn 118, Issue , 2015, Pages 81-94

Proximity biotinylation and affinity purification are complementary approaches for the interactome mapping of chromatin-associated protein complexes

Author keywords

Affinity purification coupled to mass spectrometry; BioID; Chromatin; Protein protein interactions; Proximity biotinylation; Systems biology

Indexed keywords

BIOTIN; BIOTIN PROTEIN LIGASE; CHROMATIN ASSOCIATED PROTEIN; HISTONE; LIGASE; MEDIATOR COMPLEX; NUCLEAR PROTEIN; UNCLASSIFIED DRUG; BIRA PROTEIN, E COLI; CHROMATIN; ESCHERICHIA COLI PROTEIN; MED4 PROTEIN, HUMAN; REPRESSOR PROTEIN;

EID: 84928345855     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2014.09.011     Document Type: Article
Times cited : (208)

References (41)
  • 1
    • 84862646149 scopus 로고    scopus 로고
    • Mapping physical interactions within chromatin by proteomic approaches
    • Lambert J.P., Pawson T., Gingras A.C. Mapping physical interactions within chromatin by proteomic approaches. Proteomics 2012, 12:1609-1622.
    • (2012) Proteomics , vol.12 , pp. 1609-1622
    • Lambert, J.P.1    Pawson, T.2    Gingras, A.C.3
  • 2
    • 84866401301 scopus 로고    scopus 로고
    • Mass spectrometry approaches to study mammalian kinase and phosphatase associated proteins
    • Kean M.J., Couzens A.L., Gingras A.C. Mass spectrometry approaches to study mammalian kinase and phosphatase associated proteins. Methods 2012, 57:400-408.
    • (2012) Methods , vol.57 , pp. 400-408
    • Kean, M.J.1    Couzens, A.L.2    Gingras, A.C.3
  • 3
    • 84897032710 scopus 로고    scopus 로고
    • Incorporating DNA shearing in standard affinity purification allows simultaneous identification of both soluble and chromatin-bound interaction partners
    • Lambert J.P., Tucholska M., Pawson T., Gingras A.C. Incorporating DNA shearing in standard affinity purification allows simultaneous identification of both soluble and chromatin-bound interaction partners. J Proteomics 2014, 100:55-59.
    • (2014) J Proteomics , vol.100 , pp. 55-59
    • Lambert, J.P.1    Tucholska, M.2    Pawson, T.3    Gingras, A.C.4
  • 4
    • 77951821532 scopus 로고    scopus 로고
    • A lentiviral functional proteomics approach identifies chromatin remodeling complexes important for the induction of pluripotency
    • Mak A.B., Ni Z., Hewel J.A., Chen G.I., Zhong G., Karamboulas K., et al. A lentiviral functional proteomics approach identifies chromatin remodeling complexes important for the induction of pluripotency. Mol Cell Proteomics 2010, 9:811-823.
    • (2010) Mol Cell Proteomics , vol.9 , pp. 811-823
    • Mak, A.B.1    Ni, Z.2    Hewel, J.A.3    Chen, G.I.4    Zhong, G.5    Karamboulas, K.6
  • 5
    • 84904050623 scopus 로고    scopus 로고
    • Human-chromatin-related protein interactions identify a demethylase complex required for chromosome segregation
    • Marcon E., Ni Z., Pu S., Turinsky A.L., Trimble S.S., Olsen J.B., et al. Human-chromatin-related protein interactions identify a demethylase complex required for chromosome segregation. Cell Rep 2014, 8:297-310.
    • (2014) Cell Rep , vol.8 , pp. 297-310
    • Marcon, E.1    Ni, Z.2    Pu, S.3    Turinsky, A.L.4    Trimble, S.S.5    Olsen, J.B.6
  • 6
    • 66149100528 scopus 로고    scopus 로고
    • A novel proteomics approach for the discovery of chromatin-associated protein networks
    • Lambert J.P., Mitchell L., Rudner A., Baetz K., Figeys D. A novel proteomics approach for the discovery of chromatin-associated protein networks. Mol Cell Proteomics 2009, 8:870-882.
    • (2009) Mol Cell Proteomics , vol.8 , pp. 870-882
    • Lambert, J.P.1    Mitchell, L.2    Rudner, A.3    Baetz, K.4    Figeys, D.5
  • 8
    • 84864619937 scopus 로고    scopus 로고
    • Beyond hairballs: the use of quantitative mass spectrometry data to understand protein-protein interactions
    • Gingras A.C., Raught B. Beyond hairballs: the use of quantitative mass spectrometry data to understand protein-protein interactions. FEBS Lett 2012, 586:2723-2731.
    • (2012) FEBS Lett , vol.586 , pp. 2723-2731
    • Gingras, A.C.1    Raught, B.2
  • 9
    • 84857938427 scopus 로고    scopus 로고
    • Joining forces: integrating proteomics and cross-linking with the mass spectrometry of intact complexes
    • [R111 014027]
    • Stengel F., Aebersold R., Robinson C.V. Joining forces: integrating proteomics and cross-linking with the mass spectrometry of intact complexes. Mol Cell Proteomics 2012, 11. [R111 014027].
    • (2012) Mol Cell Proteomics , vol.11
    • Stengel, F.1    Aebersold, R.2    Robinson, C.V.3
  • 10
    • 80855128256 scopus 로고    scopus 로고
    • Modularity and hormone sensitivity of the Drosophila melanogaster insulin receptor/target of rapamycin interaction proteome
    • Glatter T., Schittenhelm R.B., Rinner O., Roguska K., Wepf A., Junger M.A., et al. Modularity and hormone sensitivity of the Drosophila melanogaster insulin receptor/target of rapamycin interaction proteome. Mol Syst Biol 2011, 7:547.
    • (2011) Mol Syst Biol , vol.7 , pp. 547
    • Glatter, T.1    Schittenhelm, R.B.2    Rinner, O.3    Roguska, K.4    Wepf, A.5    Junger, M.A.6
  • 11
    • 84860270506 scopus 로고    scopus 로고
    • A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells
    • Roux K.J., Kim D.I., Raida M., Burke B. A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells. J Cell Biol 2012, 196:801-810.
    • (2012) J Cell Biol , vol.196 , pp. 801-810
    • Roux, K.J.1    Kim, D.I.2    Raida, M.3    Burke, B.4
  • 12
    • 0033846484 scopus 로고    scopus 로고
    • Function of a conserved sequence motif in biotin holoenzyme synthetases
    • Kwon K., Beckett D. Function of a conserved sequence motif in biotin holoenzyme synthetases. Protein Sci 2000, 9:1530-1539.
    • (2000) Protein Sci , vol.9 , pp. 1530-1539
    • Kwon, K.1    Beckett, D.2
  • 13
    • 84896544470 scopus 로고    scopus 로고
    • Proximity interactions among centrosome components identify regulators of centriole duplication
    • Firat-Karalar E.N., Rauniyar N., Yates J.R., Stearns T. Proximity interactions among centrosome components identify regulators of centriole duplication. Curr Biol 2014, 24:664-670.
    • (2014) Curr Biol , vol.24 , pp. 664-670
    • Firat-Karalar, E.N.1    Rauniyar, N.2    Yates, J.R.3    Stearns, T.4
  • 15
    • 84873149805 scopus 로고    scopus 로고
    • Novel bilobe components in Trypanosoma brucei identified using proximity-dependent biotinylation
    • Morriswood B., Havlicek K., Demmel L., Yavuz S., Sealey-Cardona M., Vidilaseris K., et al. Novel bilobe components in Trypanosoma brucei identified using proximity-dependent biotinylation. Eukaryot Cell 2013, 12:356-367.
    • (2013) Eukaryot Cell , vol.12 , pp. 356-367
    • Morriswood, B.1    Havlicek, K.2    Demmel, L.3    Yavuz, S.4    Sealey-Cardona, M.5    Vidilaseris, K.6
  • 16
  • 17
    • 84888100485 scopus 로고    scopus 로고
    • Protein interaction network of the mammalian Hippo pathway reveals mechanisms of kinase-phosphatase interactions
    • Couzens A.L., Knight J.D., Kean M.J., Teo G., Weiss A., Dunham W.H., et al. Protein interaction network of the mammalian Hippo pathway reveals mechanisms of kinase-phosphatase interactions. Sci Signal 2013, 6:rs15.
    • (2013) Sci Signal , vol.6
    • Couzens, A.L.1    Knight, J.D.2    Kean, M.J.3    Teo, G.4    Weiss, A.5    Dunham, W.H.6
  • 18
    • 33846844989 scopus 로고    scopus 로고
    • HORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes
    • Lamesch P., Li N., Milstein S., Fan C., Hao T., Szabo G., et al. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. Genomics 2007, 89:307-315.
    • (2007) Genomics , vol.89 , pp. 307-315
    • Lamesch, P.1    Li, N.2    Milstein, S.3    Fan, C.4    Hao, T.5    Szabo, G.6
  • 21
    • 77957947158 scopus 로고    scopus 로고
    • ProHits: integrated software for mass spectrometry-based interaction proteomics
    • Liu G., Zhang J., Larsen B., Stark C., Breitkreutz A., Lin Z.Y., et al. ProHits: integrated software for mass spectrometry-based interaction proteomics. Nat Biotechnol 2010, 28:1015-1017.
    • (2010) Nat Biotechnol , vol.28 , pp. 1015-1017
    • Liu, G.1    Zhang, J.2    Larsen, B.3    Stark, C.4    Breitkreutz, A.5    Lin, Z.Y.6
  • 23
    • 80053387432 scopus 로고    scopus 로고
    • IProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates
    • [M111 007690]
    • Shteynberg D., Deutsch E.W., Lam H., Eng J.K., Sun Z., Tasman N., et al. iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates. Mol Cell Proteomics 2011, 10. [M111 007690].
    • (2011) Mol Cell Proteomics , vol.10
    • Shteynberg, D.1    Deutsch, E.W.2    Lam, H.3    Eng, J.K.4    Sun, Z.5    Tasman, N.6
  • 24
    • 84897085529 scopus 로고    scopus 로고
    • SAINTexpress: improvements and additional features in Significance Analysis of INTeractome software
    • Teo G., Liu G., Zhang J., Nesvizhskii A.I., Gingras A.C., Choi H. SAINTexpress: improvements and additional features in Significance Analysis of INTeractome software. J Proteomics 2014, 100:37-43.
    • (2014) J Proteomics , vol.100 , pp. 37-43
    • Teo, G.1    Liu, G.2    Zhang, J.3    Nesvizhskii, A.I.4    Gingras, A.C.5    Choi, H.6
  • 25
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang da W., Sherman B.T., Lempicki R.A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009, 4:44-57.
    • (2009) Nat Protoc , vol.4 , pp. 44-57
    • Huang da, W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 28
    • 84881475940 scopus 로고    scopus 로고
    • The CRAPome: a contaminant repository for affinity purification-mass spectrometry data
    • Mellacheruvu D., Wright Z., Couzens A.L., Lambert J.P., St-Denis N.A., Li T., et al. The CRAPome: a contaminant repository for affinity purification-mass spectrometry data. Nat Methods 2013, 10:730-736.
    • (2013) Nat Methods , vol.10 , pp. 730-736
    • Mellacheruvu, D.1    Wright, Z.2    Couzens, A.L.3    Lambert, J.P.4    St-Denis, N.A.5    Li, T.6
  • 29
    • 77951819088 scopus 로고    scopus 로고
    • Systematic analysis of human protein complexes identifies chromosome segregation proteins
    • Hutchins J.R., Toyoda Y., Hegemann B., Poser I., Heriche J.K., Sykora M.M., et al. Systematic analysis of human protein complexes identifies chromosome segregation proteins. Science 2010, 328:593-599.
    • (2010) Science , vol.328 , pp. 593-599
    • Hutchins, J.R.1    Toyoda, Y.2    Hegemann, B.3    Poser, I.4    Heriche, J.K.5    Sykora, M.M.6
  • 30
    • 74549119439 scopus 로고    scopus 로고
    • Quantitative mass spectrometry of TATA binding protein-containing complexes and subunit phosphorylations during the cell cycle
    • Pijnappel W.P., Kolkman A., Baltissen M.P., Heck A., Timmers H.M. Quantitative mass spectrometry of TATA binding protein-containing complexes and subunit phosphorylations during the cell cycle. Proc Natl Acad Sci U S A 2009, 7:46.
    • (2009) Proc Natl Acad Sci U S A , vol.7 , pp. 46
    • Pijnappel, W.P.1    Kolkman, A.2    Baltissen, M.P.3    Heck, A.4    Timmers, H.M.5
  • 31
    • 84864813624 scopus 로고    scopus 로고
    • A highly efficient multifunctional tandem affinity purification approach applicable to diverse organisms
    • Ma H., McLean J.R., Chao L.F., Mana-Capelli S., Paramasivam M., Hagstrom K.A., et al. A highly efficient multifunctional tandem affinity purification approach applicable to diverse organisms. Mol Cell Proteomics 2012, 11:501-511.
    • (2012) Mol Cell Proteomics , vol.11 , pp. 501-511
    • Ma, H.1    McLean, J.R.2    Chao, L.F.3    Mana-Capelli, S.4    Paramasivam, M.5    Hagstrom, K.A.6
  • 32
    • 1542298307 scopus 로고    scopus 로고
    • Histone chaperones, a supporting role in the limelight
    • Loyola A., Almouzni G. Histone chaperones, a supporting role in the limelight. Biochim Biophys Acta 2004, 1677:3-11.
    • (2004) Biochim Biophys Acta , vol.1677 , pp. 3-11
    • Loyola, A.1    Almouzni, G.2
  • 35
    • 84872376792 scopus 로고
    • The Mediator complex and transcription elongation
    • Conaway R.C., Conaway J.W. The Mediator complex and transcription elongation. Biochim Biophys Acta 1829, 2013:69-75.
    • (1829) Biochim Biophys Acta , vol.2013 , pp. 69-75
    • Conaway, R.C.1    Conaway, J.W.2
  • 37
    • 84856290771 scopus 로고    scopus 로고
    • The centrosome in cells and organisms
    • Bornens M. The centrosome in cells and organisms. Science 2012, 335:422-426.
    • (2012) Science , vol.335 , pp. 422-426
    • Bornens, M.1
  • 38
    • 70350771277 scopus 로고    scopus 로고
    • Centrioles, centrosomes, and cilia in health and disease
    • Nigg E.A., Raff J.W. Centrioles, centrosomes, and cilia in health and disease. Cell 2009, 139:663-678.
    • (2009) Cell , vol.139 , pp. 663-678
    • Nigg, E.A.1    Raff, J.W.2
  • 39
    • 0037161731 scopus 로고    scopus 로고
    • Comparative assessment of large-scale data sets of protein-protein interactions
    • von Mering C., Krause R., Snel B., Cornell M., Oliver S.G., Fields S., et al. Comparative assessment of large-scale data sets of protein-protein interactions. Nature 2002, 417:399-403.
    • (2002) Nature , vol.417 , pp. 399-403
    • von Mering, C.1    Krause, R.2    Snel, B.3    Cornell, M.4    Oliver, S.G.5    Fields, S.6
  • 40
    • 0347473809 scopus 로고    scopus 로고
    • Gaining confidence in high-throughput protein interaction networks
    • Bader J.S., Chaudhuri A., Rothberg J.M., Chant J. Gaining confidence in high-throughput protein interaction networks. Nat Biotechnol 2004, 22:78-85.
    • (2004) Nat Biotechnol , vol.22 , pp. 78-85
    • Bader, J.S.1    Chaudhuri, A.2    Rothberg, J.M.3    Chant, J.4


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