Acetylation site specificities of lysine deacetylase inhibitors in human cells (original) (raw)
Grunstein, M. Histone acetylation in chromatin structure and transcription. Nature389, 349–352 (1997). ArticleCAS Google Scholar
Cheung, W.L., Briggs, S.D. & Allis, C.D. Acetylation and chromosomal functions. Curr. Opin. Cell Biol.12, 326–333 (2000). ArticleCAS Google Scholar
Valenzuela-Fernández, A., Cabrero, J.R., Serrador, J.M. & Sanchez-Madrid, F. HDAC6: a key regulator of cytoskeleton, cell migration and cell-cell interactions. Trends Cell Biol.18, 291–297 (2008). Article Google Scholar
Yang, X.J. & Seto, E. Lysine acetylation: codified crosstalk with other posttranslational modifications. Mol. Cell31, 449–461 (2008). ArticleCAS Google Scholar
Haberland, M., Montgomery, R.L. & Olson, E.N. The many roles of histone deacetylases in development and physiology: implications for disease and therapy. Nat. Rev. Genet.10, 32–42 (2009). ArticleCAS Google Scholar
Finkel, T., Deng, C.X. & Mostoslavsky, R. Recent progress in the biology and physiology of sirtuins. Nature460, 587–591 (2009). ArticleCAS Google Scholar
Montgomery, R.L., Hsieh, J., Barbosa, A.C., Richardson, J.A. & Olson, E.N. Histone deacetylases 1 and 2 control the progression of neural precursors to neurons during brain development. Proc. Natl. Acad. Sci. USA106, 7876–7881 (2009). ArticleCAS Google Scholar
Bolden, J.E., Peart, M.J. & Johnstone, R.W. Anticancer activities of histone deacetylase inhibitors. Nat. Rev. Drug Discov.5, 769–784 (2006). ArticleCAS Google Scholar
Marks, P.A. The clinical development of histone deacetylase inhibitors as targeted anticancer drugs. Expert Opin. Investig. Drugs19, 1049–1066 (2010). ArticleCAS Google Scholar
Archin, N.M. et al. Administration of vorinostat disrupts HIV-1 latency in patients on antiretroviral therapy. Nature487, 482–485 (2012). ArticleCAS Google Scholar
Grabiec, A.M., Tak, P.P. & Reedquist, K.A. Function of histone deacetylase inhibitors in inflammation. Crit. Rev. Immunol.31, 233–263 (2011). ArticleCAS Google Scholar
Kazantsev, A.G. & Thompson, L.M. Therapeutic application of histone deacetylase inhibitors for central nervous system disorders. Nat. Rev. Drug Discov.7, 854–868 (2008). ArticleCAS Google Scholar
Iyer, A., Fairlie, D.P. & Brown, L. Lysine acetylation in obesity, diabetes and metabolic disease. Immunol. Cell Biol.90, 39–46 (2012). ArticleCAS Google Scholar
Khan, O. & La Thangue, N.B. HDAC inhibitors in cancer biology: emerging mechanisms and clinical applications. Immunol. Cell Biol.90, 85–94 (2012). ArticleCAS Google Scholar
Xu, W.S., Parmigiani, R.B. & Marks, P.A. Histone deacetylase inhibitors: molecular mechanisms of action. Oncogene26, 5541–5552 (2007). ArticleCAS Google Scholar
Tan, J., Cang, S., Ma, Y., Petrillo, R.L. & Liu, D. Novel histone deacetylase inhibitors in clinical trials as anti-cancer agents. J. Hematol. Oncol.3, 5 (2010). Article Google Scholar
Dell′Aversana, C., Lepore, I. & Altucci, L. HDAC modulation and cell death in the clinic. Exp. Cell Res.318, 1229–1244 (2012). Article Google Scholar
Bradner, J.E. et al. Chemical phylogenetics of histone deacetylases. Nat. Chem. Biol.6, 238–243 (2010). ArticleCAS Google Scholar
Bantscheff, M. et al. Chemoproteomics profiling of HDAC inhibitors reveals selective targeting of HDAC complexes. Nat. Biotechnol.29, 255–265 (2011). ArticleCAS Google Scholar
Salisbury, C.M. & Cravatt, B.F. Activity-based probes for proteomic profiling of histone deacetylase complexes. Proc. Natl. Acad. Sci. USA104, 1171–1176 (2007). ArticleCAS Google Scholar
Ong, S.E. et al. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics1, 376–386 (2002). ArticleCAS Google Scholar
Choudhary, C. et al. Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science325, 834–840 (2009). ArticleCAS Google Scholar
Weinert, B.T. et al. Lysine succinylation is a frequently occurring modification in prokaryotes and eukaryotes and extensively overlaps with acetylation. Cell Reports4, 842–851 (2013). ArticleCAS Google Scholar
Sterner, D.E. & Berger, S.L. Acetylation of histones and transcription-related factors. Microbiol. Mol. Biol. Rev.64, 435–459 (2000). ArticleCAS Google Scholar
Drogaris, P. et al. Histone deacetylase inhibitors globally enhance h3/h4 tail acetylation without affecting h3 lysine 56 acetylation. Sci. Rep.2, 220 (2012). Article Google Scholar
Buggy, J.J. et al. CRA-024781: a novel synthetic inhibitor of histone deacetylase enzymes with antitumor activity in vitro and in vivo. Mol. Cancer Ther.5, 1309–1317 (2006). ArticleCAS Google Scholar
Balasubramanian, S. et al. A novel histone deacetylase 8 (HDAC8)-specific inhibitor PCI-34051 induces apoptosis in T-cell lymphomas. Leukemia22, 1026–1034 (2008). ArticleCAS Google Scholar
Ben-Shahar, T.R. et al. Eco1-dependent cohesin acetylation during establishment of sister chromatid cohesion. Science321, 563–566 (2008). ArticleCAS Google Scholar
Unal, E. et al. A molecular determinant for the establishment of sister chromatid cohesion. Science321, 566–569 (2008). Article Google Scholar
Zhang, J. et al. Acetylation of Smc3 by Eco1 is required for S phase sister chromatid cohesion in both human and yeast. Mol. Cell31, 143–151 (2008). ArticleCAS Google Scholar
Deardorff, M.A. et al. HDAC8 mutations in Cornelia de Lange syndrome affect the cohesin acetylation cycle. Nature489, 313–317 (2012). ArticleCAS Google Scholar
Bitterman, K.J., Anderson, R.M., Cohen, H.Y., Latorre-Esteves, M. & Sinclair, D.A. Inhibition of silencing and accelerated aging by nicotinamide, a putative negative regulator of yeast sir2 and human SIRT1. J. Biol. Chem.277, 45099–45107 (2002). ArticleCAS Google Scholar
Chen, Y. et al. Quantitative acetylome analysis reveals the roles of SIRT1 in regulating diverse substrates and cellular pathways. Mol. Cell. Proteomics11, 1048–1062 (2012). ArticleCAS Google Scholar
Kim, S.C. et al. Substrate and functional diversity of lysine acetylation revealed by a proteomics survey. Mol. Cell23, 607–618 (2006). ArticleCAS Google Scholar
Zhao, S. et al. Regulation of cellular metabolism by protein lysine acetylation. Science327, 1000–1004 (2010). ArticleCAS Google Scholar
Zhang, X. et al. HDAC6 modulates cell motility by altering the acetylation level of cortactin. Mol. Cell27, 197–213 (2007). ArticleCAS Google Scholar
Uter, W. & Schnuch, A. EMA revokes marketing authorization for bufexamac. Contact Derm.64, 235–236 (2011). Article Google Scholar
Fukuda, H., Sato, Y., Usami, N., Yokouchi, Y. & Mukai, H. Contact dermatitis caused by bufexamac sparing the eruption of herpes zoster. J. Dermatol.39, 405–407 (2012). Article Google Scholar
Jeong, J.W. et al. Regulation and destabilization of HIF-1alpha by ARD1-mediated acetylation. Cell111, 709–720 (2002). ArticleCAS Google Scholar
Dokmanovic, M., Clarke, C. & Marks, P.A. Histone deacetylase inhibitors: overview and perspectives. Mol. Cancer Res.5, 981–989 (2007). ArticleCAS Google Scholar
Yang, H. et al. Nutrient-sensitive mitochondrial NAD+ levels dictate cell survival. Cell130, 1095–1107 (2007). ArticleCAS Google Scholar
Lain, S. et al. Discovery, in vivo activity, and mechanism of action of a small-molecule p53 activator. Cancer Cell13, 454–463 (2008). ArticleCAS Google Scholar
Anderson, K.A. & Hirschey, M.D. Mitochondrial protein acetylation regulates metabolism. Essays Biochem.52, 23–35 (2012). ArticleCAS Google Scholar
Hirschey, M.D., Shimazu, T., Huang, J.Y., Schwer, B. & Verdin, E. SIRT3 regulates mitochondrial protein acetylation and intermediary metabolism. Cold Spring Harb. Symp. Quant. Biol.76, 267–277 (2011). ArticleCAS Google Scholar
Wagner, G.R. & Payne, R.M. Mitochondrial acetylation and diseases of aging. J. Aging Res.2011, 234875 (2011). Article Google Scholar
He, W., Newman, J.C., Wang, M.Z., Ho, L. & Verdin, E. Mitochondrial sirtuins: regulators of protein acylation and metabolism. Trends Endocrinol. Metab.23, 467–476 (2012). ArticleCAS Google Scholar
Eltzschig, H.K. & Carmeliet, P. Hypoxia and inflammation. N. Engl. J. Med.364, 656–665 (2011). ArticleCAS Google Scholar
Vizcaíno, J.A. et al. ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nat. Biotechnol.32, 223–226 (2014). Article Google Scholar
Nagaraj, N. et al. Deep proteome and transcriptome mapping of a human cancer cell line. Mol. Syst. Biol.7, 548 (2011). Article Google Scholar
Zhang, Y. et al. Mice lacking histone deacetylase 6 have hyperacetylated tubulin but are viable and develop normally. Mol. Cell. Biol.28, 1688–1701 (2008). ArticleCAS Google Scholar
McBurney, M.W. et al. The mammalian SIR2alpha protein has a role in embryogenesis and gametogenesis. Mol. Cell. Biol.23, 38–54 (2003). ArticleCAS Google Scholar
Vaquero, A. et al. SirT2 is a histone deacetylase with preference for histone H4 Lys 16 during mitosis. Genes Dev.20, 1256–1261 (2006). ArticleCAS Google Scholar
Mostoslavsky, R. et al. Genomic instability and aging-like phenotype in the absence of mammalian SIRT6. Cell124, 315–329 (2006). ArticleCAS Google Scholar
Rappsilber, J., Mann, M. & Ishihama, Y. Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat. Protoc.2, 1896–1906 (2007). ArticleCAS Google Scholar
Michalski, A. et al. Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer. Mol. Cell. Proteomics10, M111 011015 (2011). Article Google Scholar
Kelstrup, C.D., Young, C., Lavallee, R., Nielsen, M.L. & Olsen, J.V. Optimized fast and sensitive acquisition methods for shotgun proteomics on a quadrupole orbitrap mass spectrometer. J. Proteome Res.11, 3487–3497 (2012). ArticleCAS Google Scholar
Waanders, L.F. et al. A novel chromatographic method allows on-line reanalysis of the proteome. Mol. Cell. Proteomics7, 1452–1459 (2008). ArticleCAS Google Scholar
Elias, J.E. & Gygi, S.P. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat. Methods4, 207–214 (2007). ArticleCAS Google Scholar
Weinert, B.T. et al. Real-time PCR analysis of genes encoding tumor antigens in esophageal tumors and a cancer vaccine. Cancer Immun.9, 9 (2009). PubMedPubMed Central Google Scholar
Szklarczyk, D. et al. The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res.39, D561–D568 (2011). ArticleCAS Google Scholar
Cline, M.S. et al. Integration of biological networks and gene expression data using Cytoscape. Nat. Protoc.2, 2366–2382 (2007). ArticleCAS Google Scholar
Bindea, G. et al. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics25, 1091–1093 (2009). ArticleCAS Google Scholar
Garcia, O. et al. GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring. Bioinformatics23, 394–396 (2007). ArticleCAS Google Scholar