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Volumn 29, Issue 3, 2011, Pages 255-268

Chemoproteomics profiling of HDAC inhibitors reveals selective targeting of HDAC complexes

Author keywords

[No Author keywords available]

Indexed keywords

ANTI-INFLAMMATORIES; ANTI-INFLAMMATORY DRUGS; CATALYTIC SUBUNITS; CHEMOPROTEOMICS; DEACETYLASE; DIFFERENT EFFECTS; DOWNSTREAM TARGET; HDAC INHIBITORS; HISTONE DEACETYLASES; HYDROXAMATE; LARGE PARTS; PROTEIN COMPLEXES; SMALL MOLECULES;

EID: 79952396960     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt.1759     Document Type: Article
Times cited : (556)

References (50)
  • 1
    • 33847076849 scopus 로고    scopus 로고
    • Chromatin Modifications and Their Function
    • DOI 10.1016/j.cell.2007.02.005, PII S0092867407001845
    • Kouzarides, T. Chromatin modifications and their function. Cell 128, 693-705 (2007). (Pubitemid 46273577)
    • (2007) Cell , vol.128 , Issue.4 , pp. 693-705
    • Kouzarides, T.1
  • 2
    • 68949212379 scopus 로고    scopus 로고
    • Lysine acetylation targets protein complexes and co-regulates major cellular functions
    • Choudhary, C. et al. Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science 325, 834-840 (2009).
    • (2009) Science , vol.325 , pp. 834-840
    • Choudhary, C.1
  • 3
    • 77149148756 scopus 로고    scopus 로고
    • Regulation of cellular metabolism by protein lysine acetylation
    • Zhao, S. et al. Regulation of cellular metabolism by protein lysine acetylation. Science 327, 1000-1004 (2010).
    • (2010) Science , vol.327 , pp. 1000-1004
    • Zhao, S.1
  • 4
    • 71149106263 scopus 로고    scopus 로고
    • Switching on epigenetic therapy
    • Karberg, S. Switching on epigenetic therapy. Cell 139, 1029-1031 (2009).
    • (2009) Cell , vol.139 , pp. 1029-1031
    • Karberg, S.1
  • 5
    • 0029932598 scopus 로고    scopus 로고
    • A mammalian histone deacetylase related to the yeast transcriptional regulator Rpd3p
    • Taunton, J., Hassig, C.A. & Schreiber, S.L. A mammalian histone deacetylase related to the yeast transcriptional regulator Rpd3p. Science 272, 408-411 (1996). (Pubitemid 26138177)
    • (1996) Science , vol.272 , Issue.5260 , pp. 408-411
    • Taunton, J.1    Hassig, C.A.2    Schreiber, S.L.3
  • 6
    • 1842578986 scopus 로고    scopus 로고
    • Molecular evolution of the histone deacetylase family: Functional implications of phylogenetic analysis
    • DOI 10.1016/j.jmb.2004.02.006, PII S0022283604001408
    • Gregoretti, I.V., Lee, Y.M. & Goodson, H.V. Molecular evolution of the histone deacetylase family: functional implications of phylogenetic analysis. J. Mol. Biol. 338, 17-31 (2004). (Pubitemid 38429783)
    • (2004) Journal of Molecular Biology , vol.338 , Issue.1 , pp. 17-31
    • Gregoretti, I.V.1    Lee, Y.-M.2    Goodson, H.V.3
  • 7
    • 39749127166 scopus 로고    scopus 로고
    • The Rpd3/Hda1 family of lysine deacetylases: From bacteria and yeast to mice and men
    • DOI 10.1038/nrm2346, PII NRM2346
    • Yang, X.J. & Seto, E. The Rpd3/Hda1 family of lysine deacetylases: from bacteria and yeast to mice and men. Nat. Rev. Mol. Cell Biol. 9, 206-218 (2008). (Pubitemid 351301825)
    • (2008) Nature Reviews Molecular Cell Biology , vol.9 , Issue.3 , pp. 206-218
    • Yang, X.-J.1    Seto, E.2
  • 8
    • 56049120057 scopus 로고    scopus 로고
    • Eloquent silence: developmental functions of Class I histone deacetylases
    • DOI 10.1016/j.gde.2008.10.001, PII S0959437X08001391
    • Cunliffe, V.T. Eloquent silence: developmental functions of Class I histone deacetylases. Curr. Opin. Genet. Dev. 18, 404-410 (2008). (Pubitemid 50308559)
    • (2008) Current Opinion in Genetics and Development , vol.18 , Issue.5 , pp. 404-410
    • Cunliffe, V.T.1
  • 10
    • 0032578762 scopus 로고    scopus 로고
    • Chromatin deacetylation by an ATP-dependent nucleosome remodelling complex
    • DOI 10.1038/27699
    • Tong, J.K., Hassig, C.A., Schnitzler, G.R., Kingston, R.E. & Schreiber, S.L. Chromatin deacetylation by an ATP-dependent nucleosome remodelling complex. Nature 395, 917-921 (1998). (Pubitemid 28503435)
    • (1998) Nature , vol.395 , Issue.6705 , pp. 917-921
    • Tong, J.K.1    Hassig, C.A.2    Schnitzler, G.R.3    Kingston, R.E.4    Schreiber, S.L.5
  • 11
    • 0030916729 scopus 로고    scopus 로고
    • Histone deacetylases and SAP18, a novel polypeptide, are components of a human Sin3 complex
    • DOI 10.1016/S0092-8674(00)80216-0
    • Zhang, Y., Iratni, R., Erdjument-Bromage, H., Tempst, P. & Reinberg, D. Histone deacetylases and SAP18, A novel polypeptide, Are components of a human Sin3 complex. Cell 89, 357-364 (1997). (Pubitemid 27220880)
    • (1997) Cell , vol.89 , Issue.3 , pp. 357-364
    • Zhang, Y.1    Iratni, R.2    Erdjument-Bromage, H.3    Tempst, P.4    Reinberg, D.5
  • 12
    • 34547909260 scopus 로고    scopus 로고
    • HDAC3: Taking the SMRT-N-CoRrect road to repression
    • DOI 10.1038/sj.onc.1210612, PII 1210612
    • Karagianni, P. & Wong, J. HDAC3: taking the SMRT-N-CoRrect road to repression. Oncogene 26, 5439-5449 (2007). (Pubitemid 47255926)
    • (2007) Oncogene , vol.26 , Issue.37 , pp. 5439-5449
    • Karagianni, P.1    Wong, J.2
  • 13
    • 0035724413 scopus 로고    scopus 로고
    • The SMRT and N-CoR corepressors are activating cofactors for histone deacetylase 3
    • DOI 10.1128/MCB.21.18.6091-6101.2001
    • Guenther, M.G., Barak, O. & Lazar, M.A. The SMRT and N-CoR corepressors are activating cofactors for histone deacetylase 3. Mol. Cell. Biol. 21, 6091-6101 (2001). (Pubitemid 34263509)
    • (2001) Molecular and Cellular Biology , vol.21 , Issue.18 , pp. 6091-6101
    • Guenther, M.G.1    Barak, O.2    Lazar, M.A.3
  • 14
    • 77249087051 scopus 로고    scopus 로고
    • Chemical phylogenetics of histone deacetylases
    • Bradner, J.E. et al. Chemical phylogenetics of histone deacetylases. Nat. Chem. Biol. 6, 238-243 (2010).
    • (2010) Nat. Chem. Biol. , vol.6 , pp. 238-243
    • Bradner, J.E.1
  • 16
    • 34547684065 scopus 로고    scopus 로고
    • HDAC6, at the crossroads between cytoskeleton and cell signaling by acetylation and ubiquitination
    • DOI 10.1038/sj.onc.1210614, PII 1210614
    • Boyault, C., Sadoul, K., Pabion, M. & Khochbin, S. HDAC6, At the crossroads between cytoskeleton and cell signaling by acetylation and ubiquitination. Oncogene 26, 5468-5476 (2007). (Pubitemid 47255928)
    • (2007) Oncogene , vol.26 , Issue.37 , pp. 5468-5476
    • Boyault, C.1    Sadoul, K.2    Pabion, M.3    Khochbin, S.4
  • 17
    • 33846122993 scopus 로고    scopus 로고
    • Dimethyl sulfoxide to vorinostat: Development of this histone deacetylase inhibitor as an anticancer drug
    • DOI 10.1038/nbt1272, PII NBT1272
    • Marks, P.A. & Breslow, R. Dimethyl sulfoxide to vorinostat: development of this histone deacetylase inhibitor as an anticancer drug. Nat. Biotechnol. 25, 84-90 (2007). (Pubitemid 46087907)
    • (2007) Nature Biotechnology , vol.25 , Issue.1 , pp. 84-90
    • Marks, P.A.1    Breslow, R.2
  • 18
    • 33748451151 scopus 로고    scopus 로고
    • Anticancer activities of histone deacetylase inhibitors
    • DOI 10.1038/nrd2133, PII NRD2133
    • Bolden, J.E., Peart, M.J. & Johnstone, R.W. Anticancer activities of histone deacetylase inhibitors. Nat. Rev. Drug Discov. 5, 769-784 (2006). (Pubitemid 44348499)
    • (2006) Nature Reviews Drug Discovery , vol.5 , Issue.9 , pp. 769-784
    • Bolden, J.E.1    Peart, M.J.2    Johnstone, R.W.3
  • 22
    • 63849172494 scopus 로고    scopus 로고
    • Identifying the proteins to which small-molecule probes and drugs bind in cells
    • Ong, S.E. et al. Identifying the proteins to which small-molecule probes and drugs bind in cells. Proc. Natl. Acad. Sci. USA 106, 4617-4622 (2009).
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 4617-4622
    • Ong, S.E.1
  • 23
    • 70349624519 scopus 로고    scopus 로고
    • Proteomics strategy for quantitative protein interaction profiling in cell extracts
    • Sharma, K. et al. Proteomics strategy for quantitative protein interaction profiling in cell extracts. Nat. Methods 6, 741-744 (2009).
    • (2009) Nat. Methods , vol.6 , pp. 741-744
    • Sharma, K.1
  • 24
    • 70350412263 scopus 로고    scopus 로고
    • Revealing promiscuous drug-target interactions by chemical proteomics
    • Bantscheff, M., Scholten, A. & Heck, A.J. Revealing promiscuous drug-target interactions by chemical proteomics. Drug Discov. Today 14, 1021-1029 (2009).
    • (2009) Drug Discov. Today , vol.14 , pp. 1021-1029
    • Bantscheff, M.1    Scholten, A.2    Heck, A.J.3
  • 26
    • 52649098504 scopus 로고    scopus 로고
    • Robust and sensitive iTRAQ quantification on an LTQ Orbitrap mass spectrometer
    • Bantscheff, M. et al. Robust and sensitive iTRAQ quantification on an LTQ Orbitrap mass spectrometer. Mol. Cell. Proteomics 7, 1702-1713 (2008).
    • (2008) Mol. Cell. Proteomics , vol.7 , pp. 1702-1713
    • Bantscheff, M.1
  • 28
    • 0035851143 scopus 로고    scopus 로고
    • Regulation of global acetylation in mitosis through loss of histone acetyltransferases and deacetylases from chromatin
    • Kruhlak, M.J. et al. Regulation of global acetylation in mitosis through loss of histone acetyltransferases and deacetylases from chromatin. J. Biol. Chem. 276, 38307-38319 (2001).
    • (2001) J. Biol. Chem. , vol.276 , pp. 38307-38319
    • Kruhlak, M.J.1
  • 29
    • 77956836941 scopus 로고    scopus 로고
    • Targeted data acquisition for improved reproducibility and robustness of proteomic mass spectrometry assays
    • Savitski, M.M. et al. Targeted data acquisition for improved reproducibility and robustness of proteomic mass spectrometry assays. J. Am. Soc. Mass Spectrom. 21, 1668-1679 (2010).
    • (2010) J. Am. Soc. Mass Spectrom. , vol.21 , pp. 1668-1679
    • Savitski, M.M.1
  • 30
    • 58149089923 scopus 로고    scopus 로고
    • Pimelic diphenylamide 106 is a slow, Tight-binding inhibitor of class i histone deacetylases
    • Chou, C.J., Herman, D. & Gottesfeld, J.M. Pimelic diphenylamide 106 is a slow, Tight-binding inhibitor of class I histone deacetylases. J. Biol. Chem. 283, 35402-35409 (2008).
    • (2008) J. Biol. Chem. , vol.283 , pp. 35402-35409
    • Chou, C.J.1    Herman, D.2    Gottesfeld, J.M.3
  • 31
    • 44649140352 scopus 로고    scopus 로고
    • Atrophin recruits HDAC1/2 and G9a to modify histone H3K9 and to determine cell fates
    • DOI 10.1038/embor.2008.67, PII EMBOR200867
    • Wang, L., Charroux, B., Kerridge, S. & Tsai, C.C. Atrophin recruits HDAC1/2 and G9a to modify histone H3K9 and to determine cell fates. EMBO Rep. 9, 555-562 (2008). (Pubitemid 351772919)
    • (2008) EMBO Reports , vol.9 , Issue.6 , pp. 555-562
    • Wang, L.1    Charroux, B.2    Kerridge, S.3    Tsai, C.-C.4
  • 32
    • 57049167675 scopus 로고    scopus 로고
    • CDYL bridges REST and histone methyltransferases for gene repression and suppression of cellular transformation
    • Mulligan, P. et al. CDYL bridges REST and histone methyltransferases for gene repression and suppression of cellular transformation. Mol. Cell 32, 718-726 (2008).
    • (2008) Mol. Cell , vol.32 , pp. 718-726
    • Mulligan, P.1
  • 33
    • 78149391462 scopus 로고    scopus 로고
    • H-score, A mass accuracy driven rescoring approach for improved Peptide identification in modification rich samples
    • Savitski, M.M., Mathieson, T., Becher, I. & Bantscheff, M. H-score, A mass accuracy driven rescoring approach for improved Peptide identification in modification rich samples. J. Proteome Res. 9, 5511-5516 (2010).
    • (2010) J. Proteome Res. , vol.9 , pp. 5511-5516
    • Savitski, M.M.1    Mathieson, T.2    Becher, I.3    Bantscheff, M.4
  • 34
    • 0142214459 scopus 로고    scopus 로고
    • Examinations of the antioxidative properties of the topically administered drug bufexamac reveal new insights into its mechanism of action
    • DOI 10.1211/002235703322461569
    • Trommer, H. et al. Examinations of the antioxidative properties of the topically administered drug bufexamac reveal new insights into its mechanism of action. J. Pharm. Pharmacol. 55, 1379-1388 (2003). (Pubitemid 37321381)
    • (2003) Journal of Pharmacy and Pharmacology , vol.55 , Issue.10 , pp. 1379-1388
    • Trommer, H.1    Platzer, M.2    Raith, K.3    Wohlrab, W.4    Podhaisky, H.-P.5    Neubert, R.H.H.6
  • 35
    • 0032489015 scopus 로고    scopus 로고
    • The cell as a collection of protein machines: Preparing the next generation of molecular biologists
    • DOI 10.1016/S0092-8674(00)80922-8
    • Alberts, B. The cell as a collection of protein machines: preparing the next generation of molecular biologists. Cell 92, 291-294 (1998). (Pubitemid 28093007)
    • (1998) Cell , vol.92 , Issue.3 , pp. 291-294
    • Alberts, B.1
  • 36
    • 33644555054 scopus 로고    scopus 로고
    • Proteome survey reveals modularity of the yeast cell machinery
    • Gavin, A.C. et al. Proteome survey reveals modularity of the yeast cell machinery. Nature 440, 631-636 (2006).
    • (2006) Nature , vol.440 , pp. 631-636
    • Gavin, A.C.1
  • 37
    • 77249162697 scopus 로고    scopus 로고
    • Streamlined analysis schema for high-throughput identification of endogenous protein complexes
    • Malovannaya, A. et al. Streamlined analysis schema for high-throughput identification of endogenous protein complexes. Proc. Natl. Acad. Sci. USA 107, 2431-2436 (2010).
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 2431-2436
    • Malovannaya, A.1
  • 39
    • 43049119236 scopus 로고    scopus 로고
    • The use of diversity profiling to characterize chemical modulators of the histone deacetylases
    • Blackwell, L., Norris, J., Suto, C.M. & Janzen, W.P. The use of diversity profiling to characterize chemical modulators of the histone deacetylases. Life Sci. 82, 1050-1058 (2008).
    • (2008) Life Sci. , vol.82 , pp. 1050-1058
    • Blackwell, L.1    Norris, J.2    Suto, C.M.3    Janzen, W.P.4
  • 40
    • 77955377644 scopus 로고    scopus 로고
    • Interference with Sin3 function induces epigenetic reprogramming and differentiation in breast cancer cells
    • Farias, E.F. et al. Interference with Sin3 function induces epigenetic reprogramming and differentiation in breast cancer cells. Proc. Natl. Acad. Sci. USA 107, 11811-11816 (2010).
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 11811-11816
    • Farias, E.F.1
  • 41
    • 75149132122 scopus 로고    scopus 로고
    • Deacetylase inhibitors dissociate the histone-targeting ING2 subunit from the Sin3 complex
    • Smith, K.T., Martin-Brown, S.A., Florens, L., Washburn, M.P. & Workman, J.L. Deacetylase inhibitors dissociate the histone-targeting ING2 subunit from the Sin3 complex. Chem. Biol. 17, 65-74 (2010).
    • (2010) Chem. Biol. , vol.17 , pp. 65-74
    • Smith, K.T.1    Martin-Brown, S.A.2    Florens, L.3    Washburn, M.P.4    Workman, J.L.5
  • 42
    • 34547872069 scopus 로고    scopus 로고
    • Identification of functional domains in TdIF1 and its inhibitory mechanism for TdT activity
    • DOI 10.1111/j.1365-2443.2007.01105.x
    • Kubota, T., Maezawa, S., Koiwai, K., Hayano, T. & Koiwai, O. Identification of functional domains in TdIF1 and its inhibitory mechanism for TdT activity. Genes Cells 12, 941-959 (2007). (Pubitemid 47261989)
    • (2007) Genes to Cells , vol.12 , Issue.8 , pp. 941-959
    • Kubota, T.1    Maezawa, S.2    Koiwai, K.3    Hayano, T.4    Koiwai, O.5
  • 43
    • 43749109171 scopus 로고    scopus 로고
    • A novel histone deacetylase 8 (HDAC8)-specific inhibitor PCI-34051 induces apoptosis in T-cell lymphomas
    • DOI 10.1038/leu.2008.9, PII LEU20089
    • Balasubramanian, S. et al. A novel histone deacetylase 8 (HDAC8)-specific inhibitor PCI-34051 induces apoptosis in T-cell lymphomas. Leukemia 22, 1026-1034 (2008). (Pubitemid 351689885)
    • (2008) Leukemia , vol.22 , Issue.5 , pp. 1026-1034
    • Balasubramanian, S.1    Ramos, J.2    Luo, W.3    Sirisawad, M.4    Verner, E.5    Buggy, J.J.6
  • 44
    • 69449102464 scopus 로고    scopus 로고
    • Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes
    • Wang, Z. et al. Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes. Cell 138, 1019-1031 (2009).
    • (2009) Cell , vol.138 , pp. 1019-1031
    • Wang, Z.1
  • 45
    • 77953595441 scopus 로고    scopus 로고
    • Undesirable charge-enhancement of isobaric tagged phosphopeptides leads to reduced identification efficiency
    • Thingholm, T.E., Palmisano, G., Kjeldsen, F. & Larsen, M.R. Undesirable charge-enhancement of isobaric tagged phosphopeptides leads to reduced identification efficiency. J. Proteome Res. 9, 4045-4052 (2010).
    • (2010) J. Proteome Res. , vol.9 , pp. 4045-4052
    • Thingholm, T.E.1    Palmisano, G.2    Kjeldsen, F.3    Larsen, M.R.4
  • 47
    • 70349974261 scopus 로고    scopus 로고
    • High precision quantitative proteomics using iTRAQ on an LTQ Orbitrap: A new mass spectrometric method combining the benefits of all
    • Kocher, T. et al. High precision quantitative proteomics using iTRAQ on an LTQ Orbitrap: a new mass spectrometric method combining the benefits of all. J. Proteome Res. 8, 4743-4752 (2009).
    • (2009) J. Proteome Res. , vol.8 , pp. 4743-4752
    • Kocher, T.1
  • 48
    • 0036269973 scopus 로고    scopus 로고
    • Proteomics of the eukaryotic transcription machinery: Identification of proteins associated with components of yeast TFIID by multidimensional mass spectrometry
    • DOI 10.1128/MCB.22.13.4723-4738.2002
    • Sanders, S.L., Jennings, J., Canutescu, A., Link, A.J. & Weil, P.A. Proteomics of the eukaryotic transcription machinery: identification of proteins associated with components of yeast TFIID by multidimensional mass spectrometry. Mol. Cell. Biol. 22, 4723-4738 (2002). (Pubitemid 34620408)
    • (2002) Molecular and Cellular Biology , vol.22 , Issue.13 , pp. 4723-4738
    • Sanders, S.L.1    Jennings, J.2    Canutescu, A.3    Link, A.J.4    Weil, P.A.5
  • 49
    • 33745612095 scopus 로고    scopus 로고
    • Pvclust: An R package for assessing the uncertainty in hierarchical clustering
    • DOI 10.1093/bioinformatics/btl117
    • Suzuki, R. & Shimodaira, H. Pvclust: an R package for assessing the uncertainty in hierarchical clustering. Bioinformatics 22, 1540-1542 (2006). (Pubitemid 43985330)
    • (2006) Bioinformatics , vol.22 , Issue.12 , pp. 1540-1542
    • Suzuki, R.1    Shimodaira, H.2
  • 50
    • 34250782684 scopus 로고    scopus 로고
    • Extraction Purification and analysis of histones
    • Shechter, D., Dormann, H.L., Allis, C.D. & Hake, S.B. Extraction, Purification and analysis of histones. Nat. Protoc. 2, 1445-1457 (2007).
    • (2007) Nat. Protoc. , vol.2 , pp. 1445-1457
    • Shechter, D.1    Dormann, H.L.2    Allis, C.D.3    Hake, S.B.4


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