Double Strand Breaks Can Initiate Gene Silencing and SIRT1-Dependent Onset of DNA Methylation in an Exogenous Promoter CpG Island

PLoS Genetics - Tập 4 Số 8 - Trang e1000155
Heather M. O’Hagan1, Helai P. Mohammad1, Stephen B. Baylin1
1The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland, United States of America

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S Bjelland, 2003, Mutagenicity, toxicity and repair of DNA base damage induced by oxidation., Mutat Res, 531, 37, 10.1016/j.mrfmmm.2003.07.002

JH Hoeijmakers, 2001, Genome maintenance mechanisms for preventing cancer., Nature, 411, 366, 10.1038/35077232

R Kanaar, 1997, Recombination and joining: different means to the same ends., Genes Funct, 1, 165, 10.1046/j.1365-4624.1997.00016.x

M Shrivastav, 2007, Regulation of DNA double-strand break repair pathway choice., Cell Res, 24, 24

TH Bestor, 1998, The host defence function of genomic methylation patterns., Novartis Found Symp, 214, 187

BD Strahl, 2000, The language of covalent histone modifications., Nature, 403, 41, 10.1038/47412

SY Roth, 2001, Histone acetyltransferases., Annu Rev Biochem, 70, 81, 10.1146/annurev.biochem.70.1.81

AJ de Ruijter, 2003, Histone deacetylases (HDACs): characterization of the classical HDAC family., Biochem J, 370, 737, 10.1042/bj20021321

A Hecht, 1995, Histone H3 and H4 N-termini interact with SIR3 and SIR4 proteins: a molecular model for the formation of heterochromatin in yeast., Cell, 80, 583, 10.1016/0092-8674(95)90512-X

JS Thompson, 1994, Histone H3 amino terminus is required for telomeric and silent mating locus repression in yeast., Nature, 369, 245, 10.1038/369245a0

T Jenuwein, 2001, Translating the Histone Code., Science, 293, 1074, 10.1126/science.1063127

K Noma, 2002, Histone H3 lysine 4 methylation is mediated by Set1 and promotes maintenance of active chromatin states in fission yeast., Proc Natl Acad Sci U S A, 99, 16438, 10.1073/pnas.182436399

A Kirmizis, 2004, Silencing of human polycomb target genes is associated with methylation of histone H3 Lys 27., Genes Dev, 18, 1592, 10.1101/gad.1200204

CM Green, 2002, When repair meets chromatin. First in series on chromatin dynamics., EMBO Rep, 3, 28, 10.1093/embo-reports/kvf005

MJ Smerdon, 1978, Nucleosome rearrangement in human chromatin during UV-induced DNA- reapir synthesis., Proc Natl Acad Sci U S A, 75, 4238, 10.1073/pnas.75.9.4238

AW Bird, 2002, Acetylation of histone H4 by Esa1 is required for DNA double-strand break repair., Nature, 419, 411, 10.1038/nature01035

S Qin, 2002, Histone H3 and the histone acetyltransferase Hat1p contribute to DNA double-strand break repair., Mol Cell Biol, 22, 8353, 10.1128/MCB.22.23.8353-8365.2002

JA Downs, 2004, Binding of chromatin-modifying activities to phosphorylated histone H2A at DNA damage sites., Mol Cell, 16, 979, 10.1016/j.molcel.2004.12.003

BA Tamburini, 2005, Localized histone acetylation and deacetylation triggered by the homologous recombination pathway of double-strand DNA repair., Mol Cell Biol, 25, 4903, 10.1128/MCB.25.12.4903-4913.2005

M Altaf, 2007, Histone modifications in response to DNA damage., Mutat Res, 618, 81, 10.1016/j.mrfmmm.2006.09.009

M Falk, 2007, Chromatin dynamics during DSB repair., Biochim Biophys Acta, 1773, 1534, 10.1016/j.bbamcr.2007.07.002

LV Solovjeva, 2007, Inhibition of transcription at radiation-induced nuclear foci of phosphorylated histone H2AX in mammalian cells., Chromosome Res, 15, 787, 10.1007/s10577-007-1162-x

M Murga, 2007, Global chromatin compaction limits the strength of the DNA damage response., J Cell Biol, 178, 1101, 10.1083/jcb.200704140

O Mortusewicz, 2005, Recruitment of DNA methyltransferase I to DNA repair sites., Proc Natl Acad Sci U S A, 102, 8905, 10.1073/pnas.0501034102

J Landry, 2000, The silencing protein SIR2 and its homologs are NAD-dependent protein deacetylases., Proc Natl Acad Sci U S A, 97, 5807, 10.1073/pnas.110148297

SG Martin, 1999, Relocalization of telomeric Ku and SIR proteins in response to DNA strand breaks in yeast., Cell, 97, 621, 10.1016/S0092-8674(00)80773-4

Y Tsukamoto, 1997, Silencing factors participate in DNA repair and recombination in Saccharomyces cerevisiae., Nature, 388, 900, 10.1038/42288

M Grunstein, 1997, Molecular model for telomeric heterochromatin in yeast., Curr Opin Cell Biol, 9, 383, 10.1016/S0955-0674(97)80011-7

SJ Boulton, 1998, Components of the Ku-dependent non-homologous end-joining pathway are involved in telomeric length maintenance and telomeric silencing., Embo J, 17, 1819, 10.1093/emboj/17.6.1819

Y Tsukamoto, 1998, Double-strand break repair mediated by DNA end-joining., Genes Cells, 3, 135, 10.1046/j.1365-2443.1998.00180.x

S Imai, 2000, Transcriptional silencing and longevity protein Sir2 is an NAD-dependent histone deacetylase., Nature, 403, 795, 10.1038/35001622

G Fisher-Adams, 1995, Yeast histone H4 and H3 N-termini have different effects on the chromatin structure of the GAL1 promoter., Embo J, 14, 1468, 10.1002/j.1460-2075.1995.tb07133.x

R Murr, 2006, Histone acetylation by Trrap-Tip60 modulates loading of repair proteins and repair of DNA double-strand breaks., Nat Cell Biol, 8, 91, 10.1038/ncb1343

T Ikura, 2000, Involvement of the TIP60 histone acetylase complex in DNA repair and apoptosis., Cell, 102, 463, 10.1016/S0092-8674(00)00051-9

JY Luo, 2001, Negative control of p53 by Sir2 alpha promotes cell survival under stress., Cell, 107, 137, 10.1016/S0092-8674(01)00524-4

H Vaziri, 2001, hSIR2(SIRT1) functions as an NAD-dependent p53 deacetylase., Cell, 107, 149, 10.1016/S0092-8674(01)00527-X

E Langley, 2002, Human SIR2 deacetylates p53 and antagonizes PML/p53-induced cellular senescence., EMBO Journal, 21, 2383, 10.1093/emboj/21.10.2383

HY Cohen, 2004, Calorie restriction promotes mammalian cell survival by inducing the SIRT1 deacetylase., Science, 305, 390, 10.1126/science.1099196

K Pruitt, 2006, Inhibition of SIRT1 reactivates silenced cancer genes without loss of promoter DNA hypermethylation., PLoS Genet, 2, e40, 10.1371/journal.pgen.0020040

A Vaquero, 2004, Human SirT1 interacts with histone H1 and promotes formation of facultative heterochromatin., Mol Cell, 16, 93, 10.1016/j.molcel.2004.08.031

A Kuzmichev, 2004, Different EZH2-containing complexes target methylation of histone H1 or nucleosomal histone H3., Mol Cell, 14, 183, 10.1016/S1097-2765(04)00185-6

A Kuzmichev, 2002, Histone methyltransferase activity associated with a human multiprotein complex containing the Enhancer of Zeste protein., Genes Dev, 16, 2893, 10.1101/gad.1035902

A Kuzmichev, 2005, Composition and histone substrates of polycomb repressive group complexes change during cellular differentiation., Proc Natl Acad Sci U S A, 102, 1859, 10.1073/pnas.0409875102

A Vaquero, 2007, SIRT1 regulates the histone methyl-transferase SUV39H1 during heterochromatin formation., Nature, 450, 440, 10.1038/nature06268

JR Graff, 1995, E-cadherin expression is silenced by DNA hypermethylation in human breast and prostate carcinomas., Cancer Res, 55, 5195

P Rouet, 1994, Expression of a site-specific endonuclease stimulates homologous recombination in mammalian cells., Proc Natl Acad Sci U S A, 91, 6064, 10.1073/pnas.91.13.6064

EP Rogakou, 1999, Megabase chromatin domains involved in DNA double-strand breaks in vivo., J Cell Biol, 146, 905, 10.1083/jcb.146.5.905

TT Paull, 2000, A critical role for histone H2AX in recruitment of repair factors to nuclear foci after DNA damage., Curr Biol, 10, 886, 10.1016/S0960-9822(00)00610-2

JH Petrini, 2003, The cellular response to DNA double-strand breaks: defining the sensors and mediators., Trends Cell Biol, 13, 458, 10.1016/S0962-8924(03)00170-3

D Shore, 1998, Telomeres–unsticky ends., Science, 281, 1818, 10.1126/science.281.5384.1818

PM O'Connor, 1997, Characterization of the p53 tumor suppressor pathway in cell lines of the National Cancer Institute anticancer drug screen and correlations with the growth-inhibitory potency of 123 anticancer agents., Cancer Res, 57, 4285

SB Baylin, 2006, Epigenetic gene silencing in cancer - a mechanism for early oncogenic pathway addiction?, Nat Rev Cancer, 6, 107, 10.1038/nrc1799

AP Feinberg, 2006, The epigenetic progenitor origin of human cancer., Nat Rev Genet, 7, 21, 10.1038/nrg1748

K Ayyanathan, 2003, Regulated recruitment of HP1 to a euchromatic gene induces mitotically heritable, epigenetic gene silencing: a mammalian cell culture model of gene variegation., Genes Dev, 17, 1855, 10.1101/gad.1102803

K Myant, 2008, LSH cooperates with DNA methyltransferases to repress transcription., Mol Cell Biol, 28, 215, 10.1128/MCB.01073-07

E Cameron, 1999, Synergy of demethylation and histone deacetylase inhibition in the re-expression of genes silenced in cancer., Nature Gen, 21, 103, 10.1038/5047

H Suzuki, 2002, A genomic screen for genes upregulated by demethylation and histone deacetylase inhibition in human colorectal cancer., Nat Genet, 31, 141, 10.1038/ng892

T Furuyama, 2004, SIR2 is required for polycomb silencing and is associated with an E(Z) histone methyltransferase complex., Curr Biol, 14, 1812, 10.1016/j.cub.2004.09.060

Z Yuan, 2007, A functional link between SIRT1 deacetylase and NBS1 in DNA damage response., Cell Cycle, 6, 2869, 10.4161/cc.6.23.5026

J Jeong, 2007, SIRT1 promotes DNA repair activity and deacetylation of Ku70., Exp Mol Med, 39, 8, 10.1038/emm.2007.2

JE Ohm, 2007, A stem cell-like chromatin pattern may predispose tumor suppressor genes to DNA hypermethylation and heritable silencing., Nat Genet, 39, 237, 10.1038/ng1972

Y Schlesinger, 2007, Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer., Nat Genet, 39, 232, 10.1038/ng1950

M Widschwendter, 2007, Epigenetic stem cell signature in cancer., Nat Genet, 39, 157, 10.1038/ng1941

JE Ohm, 2007, Stem cell chromatin patterns: an instructive mechanism for DNA hypermethylation?, Cell Cycle, 6, 1040, 10.4161/cc.6.9.4210

J Espada, 2007, Epigenetic disruption of ribosomal RNA genes and nucleolar architecture in DNA methyltransferase 1 (Dnmt1) deficient cells., Nucleic Acids Res, 35, 2191, 10.1093/nar/gkm118

E Vire, 2006, The Polycomb group protein EZH2 directly controls DNA methylation., Nature, 439, 871, 10.1038/nature04431

M Shogren-Knaak, 2006, Histone H4-K16 acetylation controls chromatin structure and protein interactions., Science, 311, 844, 10.1126/science.1124000

C Cuozzo, 2007, DNA Damage, Homology-Directed Repair, and DNA Methylation., PLoS Genet, 3, e110, 10.1371/journal.pgen.0030110

MR Rountree, 2000, DNMT1 binds HDAC2 and a new co-repressor, DMAP1, to form a complex at replication foci., Nat Genet, 25, 269, 10.1038/77023

KE Bachman, 2001, Dnmt3a and Dnmt3b are transcriptional repressors that exhibit unique localization properties to heterochromatin., J Biol Chem, 276, 32282, 10.1074/jbc.M104661200

F Fuks, 2001, Dnmt3a binds deacetylases and is recruited by a sequence-specific repressor to silence transcription., Embo J, 20, 2536, 10.1093/emboj/20.10.2536

PM Vertino, 1996, De novo methylation of CpG island sequences in human fibroblasts overexpressing DNA (cytosine-5-)-methyltransferase., Mol Cell Biol, 16, 4555, 10.1128/MCB.16.8.4555

KW Jair, 2006, De novo CpG island methylation in human cancer cells., Cancer Res, 66, 682, 10.1158/0008-5472.CAN-05-1980

M Okano, 1999, DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development., Cell, 99, 247, 10.1016/S0092-8674(00)81656-6

H van Attikum, 2004, Recruitment of the INO80 complex by H2A phosphorylation links ATP-dependent chromatin remodeling with DNA double-strand break repair., Cell, 119, 777, 10.1016/j.cell.2004.11.033

AJ Morrison, 2004, INO80 and gamma-H2AX interaction links ATP-dependent chromatin remodeling to DNA damage repair., Cell, 119, 767, 10.1016/j.cell.2004.11.037

T Tsukuda, 2005, Chromatin remodelling at a DNA double-strand break site in Saccharomyces cerevisiae., Nature, 438, 379, 10.1038/nature04148

M Stucki, 2005, MDC1 directly binds phosphorylated histone H2AX to regulate cellular responses to DNA double-strand breaks., Cell, 123, 1213, 10.1016/j.cell.2005.09.038

A Jazayeri, 2004, Saccharomyces cerevisiae Sin3p facilitates DNA double-strand break repair., Proc Natl Acad Sci U S A, 101, 1644, 10.1073/pnas.0304797101

N Matsushita, 2005, Role of NAD-dependent deacetylases SIRT1 and SIRT2 in radiation and cisplatin-induced cell death in vertebrate cells., Genes Cells, 10, 321, 10.1111/j.1365-2443.2005.00836.x

K Abdelmohsen, 2007, Phosphorylation of HuR by Chk2 regulates SIRT1 expression., Mol Cell, 25, 543, 10.1016/j.molcel.2007.01.011

K De Preter, 2002, Quantification of MYCN, DDX1, and NAG gene copy number in neuroblastoma using a real-time quantitative PCR assay., Mod Pathol, 15, 159, 10.1038/modpathol.3880508

JA Fahrner, 2002, Dependence of histone modifications and gene expression on DNA hypermethylation in cancer., Cancer Res, 62, 7213

H Suzuki, 2004, Epigenetic inactivation of SFRP genes allows constitutive WNT signaling in colorectal cancer., Nat Genet, 36, 417, 10.1038/ng1330