Walboomers JMM, Jacobs MV, Manos MM, Bosch X, Kummer A, Shah KV, Snijders PJF, Peto J, Meijer CJLM, Muñoz N: Human papillomavirus is a necessary cause of invasive cervical cancer worldwide. J Pathol. 1999, 189: 12-19. 10.1002/(SICI)1096-9896(199909)189:1<12::AID-PATH431>3.0.CO;2-F.
Article
CAS
PubMed
Google Scholar
Nakahara T, Peh WL, Doorbar J, Lee D, Lambert PF: Human papillomavirus type 16 E1^E4 contributes to multiple facets of the papillomavirus life cycle. J Virol. 2005, 79: 13150-13165. 10.1128/JVI.79.20.13150-13165.2005.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rösl F, Arab A, Klevenz B, zur Hausen H: The effect of DNA methylation on gene regulation of human papillomaviruses. J Gen Virol. 1993, 74 (Pt 5): 791-801.
Article
PubMed
Google Scholar
Kalantari M, Calleja-Macias IE, Tewari D, Hagmar B, Lie K, Barrera-Saldana HA, Wiley DJ, Bernard HU: Conserved methylation patterns of human papillomavirus type 16 DNA in asymptomatic infection and cervical neoplasia. J Virol. 2004, 78: 12762-12772. 10.1128/JVI.78.23.12762-12772.2004.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kalantari M, Lee D, Calleja-Macias IE, Lambert PF, Bernard HU: Effects of cellular differentiation, chromosomal integration and 5-aza-2'-deoxycytidine treatment on human papillomavirus-16 DNA methylation in cultured cell lines. Virology. 2008, 374: 292-303. 10.1016/j.virol.2007.12.016.
Article
CAS
PubMed
PubMed Central
Google Scholar
Balderas-Loaeza A, Anaya-Saavedra G, Ramírez-Amador VA, Guido-Jiménez MC, Kalantari M, Callejas-Macias IE, Bernard HU, Garcia-Carranca A: Human papillomavirus-16 DNA methylation patterns support a causal association of the virus with oral squamous cell carcinomas. Int J Cancer. 2007, 120: 2165-2169. 10.1002/ijc.22563.
Article
CAS
PubMed
Google Scholar
Fernandez AF, Rosales C, Lopez-Nieva P, Graña O, Ballestar E, Ropero S, Espada J, Melo SA, Lujambio A, Fraga MF, Pino I, Javierre B, Carmona FJ, Acquadro F, Steenbergen RDM, Snijders PJF, Meijer CJ, Pineau P, Dejean A, Lloveras B, Capella G, Quer J, Buti M, Esteban JI, Allende H, Rodriguez-Frias F, Castellsague X, Minarovits J, Ponce J, Capello D, Gaidano G, Cigudosa JC, Gomez-Lopez G, Pisano DG, Valencia A, Piris MA, Bosch FX, Cahir-McFarland E, Kieff E, Esteller M: The dynamic DNA methylomes of double-stranded DNA viruses associated with human cancer. Genome Res. 2009, 19: 438-451.
Article
CAS
PubMed
PubMed Central
Google Scholar
Robertson KD, Ambinder RF: Methylation of the epstein-barr virus genome in normal lymphocytes. Blood. 1997, 90: 4480-4484.
CAS
PubMed
Google Scholar
Tao Q, Robertson KD: Stealth technology: How epstein-barr virus utilizes DNA methylation to cloak itself from immune detection. Clin Immunol. 2003, 109: 53-6335. 10.1016/S1521-6616(03)00198-0.
Article
CAS
PubMed
Google Scholar
Sutter D, Doerfler W: Methylation of integrated adenovirus type 12 DNA sequences in transformed cells is inversely correlated with viral gene expression. Proc Natl Acad Sci USA. 1980, 77: 253-256. 10.1073/pnas.77.1.253.
Article
CAS
PubMed
PubMed Central
Google Scholar
Badal V, Chuang LSH, Tan EHH, Badal S, Villa LL, Wheeler CM, Li BFL, Bernard HU: CpG methylation of human papillomavirus type 16 DNA in cervical cancer cell lines and in clinical specimens: Genomic hypomethylation correlates with carcinogenic progression. J Virol. 2003, 77: 6227-6234. 10.1128/JVI.77.11.6227-6234.2003.
Article
PubMed
PubMed Central
Google Scholar
Turan T, Kalantari M, Cuschieri K, Cubie HA, Skomedal H, Bernard HU: High-throughput detection of Human Papillomavirus-18 L1 gene methylation; a candidate biomarker for the progression of cervical neoplasia. Virology. 2001, 361: 185-193.
Article
Google Scholar
López Castel A, Nakamori M, Tomé S, Chitayat D, Gourdon G, Thornton CA, Pearson CE: Expanded CTG repeat demarcates a boundary for abnormal CpG methylation in myotonic dystrophy patient tissues. Hum Mol Genet. 2011, 20: 1-15. 10.1093/hmg/ddq427.
Article
PubMed
Google Scholar
Su Z, Han L, Zhao Z: Conservation and divergence of DNA methylation in eukaryotes: New insights from single base-resolution DNA methylomes. Epigenetics. 2011, 6 (2): 134-140. 10.4161/epi.6.2.13875.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jin SG, Wu X, Li AX, Pfeifer GP: Genomic mapping of 5-hydroxymethylcytosine in the human brain. Nucleic Acids Res. 2011, 39 (12): 5015-5024. 10.1093/nar/gkr120.
Article
CAS
PubMed
PubMed Central
Google Scholar
Doerfler W: In pursuit of the first recognized epigenetic signal-DNA methylation: a 1976 to 2008 synopsis. Epigenetics. 2008, 3: 125-133. 10.4161/epi.3.3.6249.
Article
PubMed
Google Scholar
Bird AP: CpG-rich islands and the function of DNA methylation. Nature. 1986, 321: 209-213. 10.1038/321209a0.
Article
CAS
PubMed
Google Scholar
Antequera F, Bird A: Number of CpG islands and genes in human and mouse. Proc Natl Acad Sci USA. 1993, 90: 11995-11999. 10.1073/pnas.90.24.11995.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schorderet DF, Gartler SM: Analysis of CpG suppression in methylated and nonmethylated species. Proc Natl Acad Sci USA. 1992, 89: 957-961. 10.1073/pnas.89.3.957.
Article
CAS
PubMed
PubMed Central
Google Scholar
Burge C, Campbell AM, Karlin S: Over- and underrepresentation of short oligonucleotides in DNA sequences. Proc Natl Acad Sci USA. 1992, 89: 1358-1362. 10.1073/pnas.89.4.1358.
Article
CAS
PubMed
PubMed Central
Google Scholar
Coulondre C, Miller JH, Farabaugh PJ, Gilbert W: Molecular basis of base substitution hotspots in Escherichia coli. Nature. 1978, 274: 775-780. 10.1038/274775a0.
Article
CAS
PubMed
Google Scholar
Scarano E, Iaccarino M, Grippo P, Parisi E: The heterogeneity of thymine methyl group origin in DNA pyrimidine isostichs of developing sea urchin embryos. Proc Natl Acad Sc USA. 1967, 57: 1394-1400. 10.1073/pnas.57.5.1394.
Article
CAS
Google Scholar
Karlin S, Doerfler W, Cardon LR: Why is CpG suppressed in the genomes of virtually all small eukaryotic viruses but not in large viruses. J Virol. 1994, 68: 2889-2897.
CAS
PubMed
PubMed Central
Google Scholar
Hoelzer K, Shackelton LA, Parrish CR: Presence and role of cytosine methylation in DNA viruses of animals. Nucleic Acids Res. 2008, 36: 2825-2837. 10.1093/nar/gkn121.
Article
CAS
PubMed
PubMed Central
Google Scholar
Herman JG, Baylin SB: Gene silencing in cancer in association with promoter hypermethylation. N Engl J Med. 2003, 349: 2042-2054. 10.1056/NEJMra023075.
Article
CAS
PubMed
Google Scholar
Gardiner-Garden M, Frommer M: CpG islands in vertebrate genomes. J Mol Biol. 1987, 196: 261-282. 10.1016/0022-2836(87)90689-9.
Article
CAS
PubMed
Google Scholar
Ponger L, Mouchiroud D: CpGProD: identifying CpG islands associated with transcription start sites in large genomic mammalian sequences. Bioinformatics. 2002, 18: 631-633. 10.1093/bioinformatics/18.4.631.
Article
CAS
PubMed
Google Scholar
Takai D, Jones PA: The CpG island searcher: a new WWW resource. In Silico Biol. 2003, 3: 235-240.
CAS
PubMed
Google Scholar
Hackenberg M, Previti C, Luque-Escamilla PL, Carpena P, Martinez-Aroza J, Oliver JL: CpG cluster: a distance-based algorithm for CpG- island detection. BMC Bioinformatics. 2006, 7: 446-458. 10.1186/1471-2105-7-446.
Article
PubMed
PubMed Central
Google Scholar
Han L, Zhao Z: CpG island or CpG clusters how to identify functional GC-rich regions in a genome?. BMC Bioinformatics. 2009, 10: 65-10.1186/1471-2105-10-65.
Article
PubMed
PubMed Central
Google Scholar
Zhao Z, Han L: CpG islands: Algorithms and applications in methylation studies. Biochem Biophysi Res Comm. 2009, 382: 643-645. 10.1016/j.bbrc.2009.03.076.
Article
CAS
Google Scholar
Han L, Su B, Li WH, Zhao Z: CpG island density and its correlations with genomic features in mammalian genomes. Genome Biology. 2008, 9 (5): R79-10.1186/gb-2008-9-5-r79.
Article
PubMed
PubMed Central
Google Scholar
Bock C, Paulsen M, Tierling S, Mikeska T, Thomas Lengauer, Walter J: CpG island methylation in human lymphocytes is highly correlated with DNA sequence, repeats, and predicted DNA structure. PLoS Genet. 2006, 2 (3): e26-10.1371/journal.pgen.0020026.
Article
PubMed
PubMed Central
Google Scholar
Shackelton LA, Parrish CR, Holmes EC: Evolutionary Basis of Codon Usage and Nucleotide Composition Bias in Vertebrate DNA Viruses. J Mol Evol. 2006, 62: 551-563. 10.1007/s00239-005-0221-1.
Article
CAS
PubMed
Google Scholar
Zhao KN, Liu WJ, Frazer IH: Codon usage bias and A + T content variation in human papillomavirus genomes. Virus Res. 2003, 98: 95-104. 10.1016/j.virusres.2003.08.019.
Article
CAS
PubMed
Google Scholar
Ho L, Chan SY, Burk RD, Das BC, Fujinaga K, Icenogle JP, Kahn T, Kiviat N, Lancaster W, Mavromara-Nazos P, Labropoulou V, Mitrani-Rosenbaum S, Norrild B, Pillai MR, Stoerker J, Syrjaenen K, Syrjaenen S, Tay SK, Villa LL, Wheeler CM, Williamson AL, Bernard HU: The Genetic Drift of Human Papillomavirus Type 16 Is a Means of Reconstructing Prehistoric Viral Spread and the Movement of Ancient Human Populations. J Virol. 1993, 67: 6413-6423.
CAS
PubMed
PubMed Central
Google Scholar
Illingworth RS, Gruenewald-Schneider U, Webb S, Kerr AR, James KD, Turner DJ, Smith C, Harrison DJ, Andrews R, Bird AP: Orphan CpG islands identify numerous conserved promoters in the mammalian genome. PLoS Genet. 2010, 6 (9): pii: e1001134
Google Scholar
Wang Q, Kennedy A, Das P, McIntosh PB, Howell SA, Isaacson ER, Hinz SA, Davy C, Doorbar J: Phosphorylation of the human papillomavirus type 16 E1-E4 protein at T57 by ERK triggers a structural change that enhances keratin binding and protein stability. J Virol. 2009, 83: 3668-3683. 10.1128/JVI.02063-08.
Article
CAS
PubMed
PubMed Central
Google Scholar
Davy CE, Jackson DJ, Wang Q, Raj K, Masterson PJ, Fenner NF, Southern S, Cuthill S, Millar JBA, Doorbar J: Identification of a G2 arrest domain in the E1^E4 protein of human papillomavirus type 16. J Virol. 2002, 76: 9806-9818. 10.1128/JVI.76.19.9806-9818.2002.
Article
CAS
PubMed
PubMed Central
Google Scholar
Peh WL, Middleton K, Christensen N, Nicholls P, Egawa K, Sotlar K, Brandsma J, Percival A, Lewis J, Liu WJ, Doorbar J: Life cycle heterogeneity in animal models of human papillomavirus-associated disease. J Virol. 2002, 76: 10401-10416. 10.1128/JVI.76.20.10401-10416.2002.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bell I, Martin A, Roberts S: The E1^E4 protein of human papillomavirus interacts with the serine-arginine-specific protein kinase SRPK1. J Virol. 2007, 81: 5437-5448. 10.1128/JVI.02609-06.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wilson R, Fehrmann F, Laimins LA: Role of the E1^E4 Protein in the Differentiation-dependent life cycle of human papillomavirus type 31. J Virol. 2005, 79: 6732-6740. 10.1128/JVI.79.11.6732-6740.2005.
Article
CAS
PubMed
PubMed Central
Google Scholar
Morgan MT, Maiti A, Fitzgerald ME, Drohat AC: Stoichiometry and affinity for thymine DNA glycosylase binding to specific and nonspecific DNA. Nucleic Acids Res. 2011, 39: 2319-2329. 10.1093/nar/gkq1164.
Article
CAS
PubMed
Google Scholar
Screaton RA, Kiessling S, Sansom OJ, Millar CB, Maddison K, Bird A, Clarke AR, Frisch SM: Fas-associated death domain protein interacts with methyl-CpG binding domain protein 4: A potential link between genome surveillance and apoptosis. Proc Natl Acad Sc USA. 2003, 100: 5211-5216. 10.1073/pnas.0431215100.
Article
CAS
Google Scholar
De Villiers EM, Fauquet C, Broker TR, Bernard HU, zur Hausen H: Classification of papillomaviruses. Virology. 2004, 324: 17-27. 10.1016/j.virol.2004.03.033.
Article
CAS
PubMed
Google Scholar
Diallo AB, Badescu D, Blanchette M, Makarenkov V: A Whole Genome Study and Identification of Specific Carcinogenic Regions of the Human Papilloma Viruses. J Comp Biol. 2009, 16: 1461-1473. 10.1089/cmb.2009.0091.
Article
CAS
Google Scholar
Tatusov T, Tatusov R: "ORF finder" Online Software. [http://www.ncbi.nlm.nih.gov]
Wessa P: Free Statistics Software, Office for Research, Development and Education, version 1.1.23-r5. [http://wessa.net/]
Soper DS: "The Free Statistics Calculators Website", Online Software. [http://danielsoper.com/statcalc3/default.aspx]