Basic Nuclear Processes Affected by Histone Acetyltransferases and Histone Deacetylase Inhibitors

• Lanctôt C , CheutinT, CremerM, CavalliG, CremerT Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions. Nat. Rev. Genet.8 , 104–115 (2007).
   PubMed Web of Science ®Google Scholar
• Snustad DP , SimmonsMJ. Principles of Genetics. John Wiley and Sons, NY, USA (2009).
   Google Scholar
• Cremer T , CremerC. Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat. Rev. Genet.2 , 292–301 (2001).
   PubMed Web of Science ®Google Scholar
• Campbell N , ReeceAP. Biology. Pearson, Education Inc., CA, USA (2008).
   Google Scholar
• Almouzni G , ProbstAV. Heterochromatin maintenance and establishment: lessons from the mouse pericentromere. Nucleus2 , 332–338 (2011).
   PubMed Web of Science ®Google Scholar
• Bártová E , KrejčíJ, HarničarováA, GaliováG, KozubekS. Histone modifications and nuclear architecture: a review. J. Histochem. Cytochem.56 , 711–721 (2008).
   PubMed Web of Science ®Google Scholar
• Casas-Delucchi CS , BreroA, RahnHP et al. Histone acetylation controls the inactive X chromosome replication dynamics. Nat. Commun. 2 , 222 (2011).
   PubMed Web of Science ®Google Scholar
• Turner BM . Reading signals on the nucleosome with a new nomenclature for modified histones. Nat. Struct. Mol. Biol.12 , 110–112 (2005).
   PubMed Web of Science ®Google Scholar
• Jenuwein T . The epigenetic magic of histone lysine methylation. FEBS J.273 , 3121–3135 (2006).
   PubMed Web of Science ®Google Scholar
• Kouzarides T . Chromatin modifications and their function. Cell128 , 693–705 (2007).
   PubMed Web of Science ®Google Scholar
• Martinet N , BertrandP. Interpreting clinical assays for histone deacetylase inhibitors. Cancer Manag. Res.3 , 117–141 (2011).
   PubMedGoogle Scholar
• Santos-Rosa H , CaldasC. Chromatin modifier enzymes, the histone code and cancer. Eur. J. Cancer41 , 2381–2402 (2005).
   PubMed Web of Science ®Google Scholar
• Ghizzoni M , HaismaHJ, MaarsinghH, DekkerFJ. Histone acetyltransferases are crucial regulators in NF-κB mediated inflammation. Drug Discov. Today16 , 504–511 (2011).
   PubMed Web of Science ®Google Scholar
• Foltánková V , LegartováS, KozubekS, BártováE. Tumor-specific histone signature and DNA methylation in multiple myeloma and leukemia cells. Neoplasma59 , 450–462 (2012).
   PubMed Web of Science ®Google Scholar
• Bártová E , KrejčíJ, HarnicarováA, KozubekS. Differentiation of human embryonic stem cells induces condensation of chromosome territories and formation of heterochromatin protein 1 foci. Differentiation76 , 24–32 (2008).
   PubMed Web of Science ®Google Scholar
• Marks PA , RichonVM, RifkindRA. Histone deacetylase inhibitors: inducers of differentiation or apoptosis of transformed cells. J. Natl Cancer Inst.92 , 1210–1216 (2000).
   PubMed Web of Science ®Google Scholar
• Khan N , JeffersM, KumarS et al. Determination of the class and isoform selectivity of small-molecule histone deacetylase inhibitors. Biochem. J. 409 , 581–589 (2008).
   PubMed Web of Science ®Google Scholar
• LaBonte MJ , WilsonPM, FazzoneW, GroshenS, LenzHJ, LadnerRD. DNA microarray profiling of genes differentially regulated by the histone deacetylase inhibitors vorinostat and LBH589 in colon cancer cell lines. BMC Med. Genomics2 , 67 (2009).
   PubMed Web of Science ®Google Scholar
• Ghizzoni M , WuJ, GaoT, HaismaHJ, DekkerFJ, George Zheng Y. 6-alkylsalicylates are selective Tip60 inhibitors and target the acetyl-CoA binding site. Eur. J. Med. Chem.47 , 337–344 (2012).
   PubMed Web of Science ®Google Scholar
• Bolstad BM , IrizarryRA, AstrandM, SpeedTP. A comparison of normalization methods for high density oligonucleotide array data based on bias and variance. Bioinformatics19 , 185–193 (2003).
   PubMed Web of Science ®Google Scholar
• Irizarry RA , BolstadBM, CollinF et al. Summaries of affymetrix GeneChip probe level data. Nucleic Acids Res. 31 , e15 (2003).
   PubMed Web of Science ®Google Scholar
• Smyth GK . Limma: linear models for microarray data. In: Bioinformatics and Computational Biology Solutions Using R and Bioconductor. Gentleman R, Carey V, Dudoit S, Irizarry R, Huber W (Eds). Springer, NY, USA, 397–420 (2005).
   Google Scholar
• Storey JD . The positive false discovery rate: a Bayesian interpretation and the q-value. Ann. Stat.31 , 2013–2035 (2003).
   Web of Science ®Google Scholar
• Kanehisa M , GotoS. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res.28 , 27–30 (2000).
   PubMed Web of Science ®Google Scholar
• Ashburner M , BallCA, BlakeJA et al. Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat. Genet. 25 , 25–29 (2000).
   PubMed Web of Science ®Google Scholar
• Tarca AL , DraghiciS, KhatriP et al. A signaling pathway impact analysis for microarray experiments. Bioinformatics 25 , 75–82 (2009).
   PubMed Web of Science ®Google Scholar
• Peart M , SmythG, van Laar R et al. Identification and functional significance of genes regulated by structurally different histone deacetylase inhibitors. Proc. Natl Acad. Sci. USA102 , 3697–3702 (2005).
   PubMed Web of Science ®Google Scholar
• Gu W , ShiXL, RoederRG. Synergistic activation of transcription by CBP and p53. Nature387 , 819–823 (1997).
   PubMed Web of Science ®Google Scholar
• Imhof A , YangXJ, OgryzkoVV, NakataniY, WolffeAP, GeH. Acetylation of general transcription factors by histone acetyltransferases. Curr. Biol.7 , 689–692 (1997).
   PubMed Web of Science ®Google Scholar
• Marks PA . The clinical development of histone deacetylase inhibitors as targeted anticancer drugs. Expert Opin. Investig. Drugs19 , 1049–1066 (2010).
   PubMed Web of Science ®Google Scholar
• Bártová E , PacherníkJ, HarničarováA et al. Nuclear levels and patterns of histone H3 modification and HP1 proteins after inhibition of histone deacetylases. J. Cell Sci. 118(Pt 21) , 5035–5046 (2005).
   PubMed Web of Science ®Google Scholar
• Harničarová A , KozubekS, PacherníkJ, KrejčíJ, BártováE. Distinct nuclear arrangement of active and inactive c-myc genes in control and differentiated colon carcinoma cells. Exp. Cell Res.312 , 4019–4035 (2006).
   PubMed Web of Science ®Google Scholar
• Bártová E , PacherníkJ, KozubíkA, KozubekS. Differentiation-specific association of HP1α and HP1β with chromocentres is correlated with clustering of TIF1β at these sites. Histochem. Cell Biol.27 , 375–388 (2007).
   Google Scholar
• Gilmore TD . Introduction to NF-κB: players, pathways, perspectives. Oncogene25 , 6680–6684 (2006).
   PubMed Web of Science ®Google Scholar
• Kawahara TL , MichishitaE, AdlerAS et al. SIRT6 links histone H3 lysine 9 deacetylation to NF-κB-dependent gene expression and organismal life span. Cell 136 , 62–74 (2009).
   PubMed Web of Science ®Google Scholar
• Ashburner BP , WesterheideSD, BaldwinAS Jr. The p65 (RelA) subunit of NF-κB interacts with the histone deacetylase (HDAC) corepressors HDAC1 and HDAC2 to negatively regulate gene expression. Mol. Cell Biol.21 , 7065–7077 (2001).
   PubMed Web of Science ®Google Scholar
• Velasco-Miguel S , BuckbinderL, JeanP et al. PA26, a novel target of the p53 tumor suppressor and member of the GADD family of DNA damage and growth arrest inducible genes. Oncogene 18 , 127–137 (1999).
   PubMed Web of Science ®Google Scholar
• Budanov AV , ShoshaniT, FaermanA et al. Identification of a novel stress-responsive gene Hi95 involved in regulation of cell viability. Oncogene 21 , 6017–6031 (2002).
   PubMed Web of Science ®Google Scholar
• Hay N . p53 strikes mTORC1 by employing Sestrins. Cell Metab.8 , 184–185 (2008).
   PubMed Web of Science ®Google Scholar
• Ma Y , FanS, HuC et al. BRCA1 regulates acetylation and ubiquitination of estrogen receptor-α. Mol. Endocrinol. 24 , 76–90 (2010).
   PubMed Web of Science ®Google Scholar
• Chen MY , LiaoWS, LuZ et al. Decitabine and suberoylanilide hydroxamic acid (SAHA) inhibit growth of ovarian cancer cell lines and xenografts while inducing expression of imprinted tumor suppressor genes, apoptosis, G2/M arrest, and autophagy. Cancer 117 , 4424–4438 (2011).
   PubMed Web of Science ®Google Scholar
• Kumagai T , WakimotoN, YinD et al. Histone deacetylase inhibitor, suberoylanilide hydroxamic acid (vorinostat, SAHA) profoundly inhibits the growth of human pancreatic cancer cells. Int. J. Cancer 121 , 656–665 (2007).
   PubMed Web of Science ®Google Scholar
• Lauricella M , CiraoloA, CarlisiD, VentoR, TesoriereG. SAHA/TRAIL combination induces detachment and anoikis of MDA-MB231 and MCF-7 breast cancer cells. Biochimie94 , 287–299 (2012).
   PubMed Web of Science ®Google Scholar
• Jackson SP , BartekJ. The DNA-damage response in human biology and disease. Nature461 , 1071–1078 (2009).
   PubMed Web of Science ®Google Scholar
• Misteli T , SoutoglouE. The emerging role of nuclear architecture in DNA repair and genome maintenance. Nat. Rev. Mol. Cell Biol.10 , 243–254 (2009).
   PubMed Web of Science ®Google Scholar
• Soria G , AlmouzniG. Differential contribution of HP1 proteins to DNA end resection and homology-directed repair. Cell Cycle12 , 422–429 (2013).
   PubMed Web of Science ®Google Scholar
• Luco RF , PanQ, TominagaK, BlencoweBJ, Pereira-SmithOM, MisteliT. Regulation of alternative splicing by histone modifications. Science327 , 996–1000 (2010).
   PubMed Web of Science ®Google Scholar
• Miller KM , JacksonSP. Histone marks: repairing DNA breaks within the context of chromatin. Biochem. Soc. Trans.40 , 370–376 (2012).
   PubMed Web of Science ®Google Scholar
• Rea MA , GreggJP, QinQ, PhillipsMA, RiceRH. Global alteration of gene expression in human keratinocytes by inorganic arsenic. Carcinogenesis24 , 747–756 (2003).
   PubMed Web of Science ®Google Scholar
• Trevisan R , DapraiL, PaloschiL, VajenteN, Chieco-BianchiL, SaggioroD. Antiapoptotic effect of human T-cell leukemia virus type 1 tax protein correlates with its creb transcriptional activity. Exp. Cell Res.312 , 139–1400 (2006).
   Google Scholar

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• ArrayExpress. ArrayExpress –functional genomics data. www.ebi.ac.uk/arrayexpress
   Google Scholar