Basic nuclear processes affected by histone acetyltransferases and histone deacetylase inhibitors

Epigenomics

Volumn 5, Issue 4, 2013, Pages 379-396

  Legartová, Soňa ^a   Stixová, Lenka ^a   Strnad, Hynek ^b   Kozubek, Stanislav ^a   Martinet, Nadine ^c   Dekker, Frank J ^d   Franek, Michal ^a   Bártová, Eva ^a  

^a INSTITUTE OF BIOPHYSICS   (Czech Republic)

^b INSTITUTE OF MOLECULAR GENETICS   (Czech Republic)

^c UNIVERSITÉ DE NICE SOPHIA ANTIPOLIS   (France)

^d UNIVERSITY OF GRONINGEN   (Netherlands)

Author keywords

cDNA microarray; DNA repair; epi drug; HAT; HDAC; histone acetylation; nuclear process; p53; replication; splicing; transcription; tumor cell

Indexed keywords

ACYLTRANSFERASE INHIBITOR; COMPLEMENTARY DNA; HISTONE ACETYLTRANSFERASE; HISTONE DEACETYLASE INHIBITOR; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; MG 149; PROTEIN P53; UNCLASSIFIED DRUG; VORINOSTAT;

APOPTOSIS; ARTICLE; CELL VIABILITY; DNA REPAIR; EMBRYONIC STEM CELL; GENE EXPRESSION; HISTONE ACETYLATION; HUMAN; HUMAN CELL; HUMAN CELL CULTURE; INTRACELLULAR SIGNALING; MULTIPLE MYELOMA; MYELOMA CELL; PRIORITY JOURNAL; RECEPTOR DOWN REGULATION; RNA ISOLATION; SPLICEOSOME; WESTERN BLOTTING;

ACETYLATION; APOPTOSIS; BRCA2 PROTEIN; CELL LINE, TUMOR; CELL NUCLEUS; DNA REPAIR; EPIGENESIS, GENETIC; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HISTONE ACETYLTRANSFERASES; HISTONE DEACETYLASE INHIBITORS; HISTONES; HUMANS; HYDROXAMIC ACIDS; K562 CELLS; NF-KAPPA B; NUCLEAR PROTEINS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RAD51 RECOMBINASE; RNA; SIGNAL TRANSDUCTION; SPLICEOSOMES; TRANSCRIPTION FACTORS; TUMOR SUPPRESSOR PROTEIN P53;

EID: 84881111643     PISSN: 17501911     EISSN: 1750192X     Source Type: Journal    
DOI: 10.2217/epi.13.38     Document Type: Article

References (50)

1. Lanctôt C, Cheutin T, Cremer M, Cavalli G, Cremer T. Dynamic genome architecture in the nuclear space: Regulation of gene expression in three dimensions. Nat. Rev. Genet. 8, 104-115 (2007
2. Snustad DP, Simmons MJ. Principles of Genetics. John Wiley and Sons, NY, USA (2009
3. Cremer T, Cremer C. Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat. Rev. Genet. 2, 292-301 (2001
4. Campbell N, Reece AP. Biology. Pearson, Education Inc., CA, USA (2008
5. Almouzni G, Probst AV. Heterochromatin maintenance and establishment: Lessons from the mouse pericentromere. Nucleus 2, 332-338 (2011
6. Bártová E, Krejčí J, Harnič arová A, Galiová G, Kozubek S. Histone modifications and nuclear architecture: A review. J. Histochem. Cytochem. 56, 711-721 (2008
7. Casas-Delucchi CS, Brero A, Rahn HP et al. Histone acetylation controls the inactive X chromosome replication dynamics. Nat. Commun. 2, 222 (2011
8. Turner BM. Reading signals on the nucleosome with a new nomenclature for modified histones. Nat. Struct. Mol. Biol. 12, 110-112 (2005
9. Jenuwein T. The epigenetic magic of histone lysine methylation. FEBS J. 273, 3121-3135 (2006
10. Kouzarides T. Chromatin modifications and their function. Cell 128, 693-705 (2007
11. Martinet N, Bertrand P. Interpreting clinical assays for histone deacetylase inhibitors. Cancer Manag. Res. 3, 117-141 (2011
12. Santos-Rosa H, Caldas C. Chromatin modifier enzymes, the histone code and cancer. Eur. J. Cancer 41, 2381-2402 (2005
13. Ghizzoni M, Haisma HJ, Maarsingh H, Dekker FJ. Histone acetyltransferases are crucial regulators in NF-kB mediated inflammation. Drug Discov. Today 16, 504-511 (2011
14. Foltánková V, Legartová S, Kozubek S, Bártová E. Tumor-specific histone signature and DNA methylation in multiple myeloma and leukemia cells. Neoplasma 59, 450-462 (2012
15. Bártová E, Krejčí J, Harnicarová A, Kozubek S. Differentiation of human embryonic stem cells induces condensation of chromosome territories and formation of heterochromatin protein 1 foci. Differentiation 76, 24-32 (2008
16. Marks PA, Richon VM, Rifkind RA. Histone deacetylase inhibitors: Inducers of differentiation or apoptosis of transformed cells. J. Natl Cancer Inst. 92, 1210-1216 (2000
17. Khan N, Jeffers M, Kumar S et al. Determination of the class and isoform selectivity of small-molecule histone deacetylase inhibitors. Biochem. J. 409, 581-589 (2008
18. LaBonte MJ, Wilson PM, Fazzone W, Groshen S, Lenz HJ, Ladner RD. DNA microarray profiling of genes differentially regulated by the histone deacetylase inhibitors vorinostat and LBH589 in colon cancer cell lines. BMC Med. Genomics 2, 67 (2009
19. Ghizzoni M, Wu J, Gao T, Haisma HJ, Dekker FJ, George Zheng Y. 6-Alkylsalicylates are selective Tip60 inhibitors and target the acetyl-CoA binding site. Eur. J. Med. Chem. 47, 337-344 (2012
20. Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on bias and variance. Bioinformatics 19, 185-193 (2003
21. Irizarry RA, Bolstad BM, Collin F et al. Summaries of affymetrix GeneChip probe level data. Nucleic Acids Res. 31, e15 (2003
22. 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
23. Storey JD. The positive false discovery rate: A Bayesian interpretation and the q-value. Ann. Stat. 31, 2013-2035 (2003
24. Kanehisa M, Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28, 27-30 (2000
25. Ashburner M, Ball CA, Blake JA et al. Gene ontology: Tool for the unification of biology. The gene ontology consortium. Nat. Genet. 25, 25-29 (2000
26. Tarca AL, Draghici S, Khatri P et al. A signaling pathway impact analysis for microarray experiments. Bioinformatics 25, 75-82 (2009
27. Peart M, Smyth G, van Laar R et al. Identification and functional significance of genes regulated by structurally different histone deacetylase inhibitors. Proc. Natl Acad. Sci. USA 102, 3697-3702 (2005
28. Gu W, Shi XL, Roeder RG Synergistic activation of transcription by CBP and p53. Nature 387, 819-823 (1997
29. Imhof A, Yang XJ, Ogryzko VV, Nakatani Y, Wolffe AP, Ge H. Acetylation of general transcription factors by histone acetyltransferases. Curr. Biol. 7, 689-692 (1997
30. Marks PA. The clinical development of histone deacetylase inhibitors as targeted anticancer drugs. Expert Opin. Investig. Drugs 19, 1049-1066 (2010
31. Bártová E, Pacherník J, Harničarová A 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
32. Harničarová A, Kozubek S, Pacherník J, Krejčí J, Bártová E. Distinct nuclear arrangement of active and inactive c-myc genes in control and differentiated colon carcinoma cells. Exp. Cell Res. 312, 4019-4035 (2006
33. Bártová E, Pacherník J, Kozubík A, Kozubek S. Differentiation-specific association of HP1a and HP1b with chromocentres is correlated with clustering of TIF1b at these sites. Histochem. Cell Biol. 27, 375-388 (2007
34. Gilmore TD. Introduction to NF-kB: Players, pathways, perspectives. Oncogene 25, 6680-6684 (2006
35. Kawahara TL, Michishita E, Adler AS et al. SIRT6 links histone H3 lysine 9 deacetylation to NF-kB-dependent gene expression and organismal life span. Cell 136, 62-74 (2009
36. Ashburner BP, Westerheide SD, Baldwin AS Jr. The p65 (RelA) subunit of NF-kB interacts with the histone deacetylase (HDAC) corepressors HDAC1 and HDAC2 to negatively regulate gene expression. Mol. Cell Biol. 21, 7065-7077 (2001
37. Velasco-Miguel S, Buckbinder L, Jean P 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
38. Budanov AV, Shoshani T, Faerman A et al. Identification of a novel stress-responsive gene Hi95 involved in regulation of cell viability. Oncogene 21, 6017-6031 (2002
39. Hay N. p53 strikes mTORC1 by employing Sestrins. Cell Metab. 8, 184-185 (2008
40. Ma Y, Fan S, Hu C et al. BRCA1 regulates acetylation and ubiquitination of estrogen receptor-A. Mol. Endocrinol. 24, 76-90 (2010
41. Chen MY, Liao WS, Lu Z 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
42. Kumagai T, Wakimoto N, Yin D 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
43. Lauricella M, Ciraolo A, Carlisi D, Vento R, Tesoriere G. SAHA/TRAIL combination induces detachment and anoikis of MDA-MB231 and MCF-7 breast cancer cells. Biochimie 94, 287-299 (2012
44. Jackson SP, Bartek J. The DNA-damage response in human biology and disease. Nature 461, 1071-1078 (2009
45. Misteli T, Soutoglou E. The emerging role of nuclear architecture in DNA repair and genome maintenance. Nat. Rev. Mol. Cell Biol. 10, 243-254 (2009
46. Soria G, Almouzni G. Differential contribution of HP1 proteins to DNA end resection and homology-directed repair. Cell Cycle 12, 422-429 (2013
47. Luco RF, Pan Q, Tominaga K, Blencowe BJ, Pereira-Smith OM, Misteli T. Regulation of alternative splicing by histone modifications. Science 327, 996-1000 (2010
48. Miller KM, Jackson SP. Histone marks: Repairing DNA breaks within the context of chromatin. Biochem. Soc. Trans. 40, 370-376 (2012
49. Rea MA, Gregg JP, Qin Q, Phillips MA, Rice RH. Global alteration of gene expression in human keratinocytes by inorganic arsenic. Carcinogenesis 24, 747-756 (2003
50. Trevisan R, Daprai L, Paloschi L, Vajente N, Chieco-Bianchi L, Saggioro D. 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