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Volumn 24, Issue 5, 2014, Pages 761-774

Recurrent epimutations activate gene body promoters in primary glioblastoma

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE H3; PROTEIN P73; DNA BINDING PROTEIN; GLI3 PROTEIN, HUMAN; KRUPPEL LIKE FACTOR; NERVE PROTEIN; NUCLEAR PROTEIN; TELOMERASE; TERT PROTEIN, HUMAN; TUMOR SUPPRESSOR PROTEIN; TUMOR SUPPRESSOR PROTEIN P73;

EID: 84899893679     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.164707.113     Document Type: Article
Times cited : (35)

References (79)
  • 3
    • 33749039999 scopus 로고    scopus 로고
    • Genome-wide hypomethylation in human glioblastomas associated with specific copy number alteration, methylenetetrahydrofolate reductase allele status, and increased proliferation
    • Cadieux B, Ching TT, VandenBerg SR, Costello JF. 2006. Genome-wide hypomethylation in human glioblastomas associated with specific copy number alteration, methylenetetrahydrofolate reductase allele status, and increased proliferation. Cancer Res 66: 8469-8476.
    • (2006) Cancer Res , vol.66 , pp. 8469-8476
    • Cadieux, B.1    Ching, T.T.2    VandenBerg, S.R.3    Costello, J.F.4
  • 6
    • 0037112364 scopus 로고    scopus 로고
    • Loss of imprinting in colorectal cancer linked to hypomethylation of h19 and igf2
    • Cui H, Onyango P, Brandenburg S,Wu Y, Hsieh C-L, Feinberg AP. 2002. Loss of imprinting in colorectal cancer linked to hypomethylation of H19 and IGF2. Cancer Res 62: 6442-6446.
    • (2002) Cancer Res , vol.62 , pp. 6442-6446
    • Cui, H.1    Onyango, P.2    Brandenburg, S.3    Wu, Y.4    Hsieh, C.-L.5    Feinberg, A.P.6
  • 7
    • 0029957792 scopus 로고    scopus 로고
    • The activation of human gene mage-1 in tumor cells is correlated with genome-wide demethylation
    • De Smet C, De Backer O, Faraoni I, Lurquin C, Brasseur F, Boon T. 1996. The activation of human gene MAGE-1 in tumor cells is correlated with genome-wide demethylation. Proc Natl Acad Sci 93: 7149-7153.
    • (1996) Proc Natl Acad Sci , vol.93 , pp. 7149-7153
    • De Smet, C.1    De Backer, O.2    Faraoni, I.3    Lurquin, C.4    Brasseur, F.5    Boon, T.6
  • 8
    • 84867345057 scopus 로고    scopus 로고
    • Chance: Comprehensive software for quality control and validation of chip-seq data
    • Diaz A, Nellore A, Song JS. 2012. CHANCE: comprehensive software for quality control and validation of ChIP-seq data. Genome Biol 13: R98.
    • (2012) Genome Biol , vol.13
    • Diaz, A.1    Nellore, A.2    Song, J.S.3
  • 10
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of dna elements in the human genome
    • The ENCODE Project Consortium
    • The ENCODE Project Consortium. 2012. An integrated encyclopedia of DNA elements in the human genome. Nature 489: 57-74.
    • (2012) Nature , vol.489 , pp. 57-74
  • 13
    • 0020699979 scopus 로고
    • Hypomethylation distinguishes genes of some human cancers fromtheir normal counterparts
    • Feinberg AP, Vogelstein B. 1983. Hypomethylation distinguishes genes of some human cancers fromtheir normal counterparts. Nature 301: 89-92.
    • (1983) Nature , vol.301 , pp. 89-92
    • Feinberg, A.P.1    Vogelstein, B.2
  • 15
    • 0035407651 scopus 로고    scopus 로고
    • Bisulfite genomic sequencing: Systematic investigation of critical experimental parameters
    • Grunau C, Clark SJ, Rosenthal A. 2001. Bisulfite genomic sequencing: systematic investigation of critical experimental parameters. Nucleic Acids Res 29: E65.
    • (2001) Nucleic Acids Res , vol.29
    • Grunau, C.1    Clark, S.J.2    Rosenthal, A.3
  • 19
    • 0020951126 scopus 로고
    • Altered methionine metabolism, dna methylation and oncogene expression in carcinogenesis. A review and synthesis
    • Hoffman RM. 1984. Altered methionine metabolism, DNA methylation and oncogene expression in carcinogenesis. A review and synthesis. Biochim Biophys Acta 738: 49-87.
    • (1984) Biochim Biophys Acta , vol.738 , pp. 49-87
    • Hoffman, R.M.1
  • 22
    • 84868674716 scopus 로고    scopus 로고
    • Alternatively spliced telomerase reverse transcriptase variants lacking telomerase activity stimulate cell proliferation
    • Hrdlickova R, Nehyba J, Bose HR Jr. 2012. Alternatively spliced telomerase reverse transcriptase variants lacking telomerase activity stimulate cell proliferation. Mol Cell Biol 32: 4283-4296.
    • (2012) Mol Cell Biol , vol.32 , pp. 4283-4296
    • Hrdlickova, R.1    Nehyba, J.2    Bose Jr., H.R.3
  • 25
    • 0036468249 scopus 로고    scopus 로고
    • Possible oncogenic potential of dnp73: A newly identified isoform of human p73
    • Ishimoto O, Kawahara C, Enjo K, Obinata M, Nukiwa T, Ikawa S. 2002. Possible oncogenic potential of DNp73: a newly identified isoform of human p73. Cancer Res 62: 636-641.
    • (2002) Cancer Res , vol.62 , pp. 636-641
    • Ishimoto, O.1    Kawahara, C.2    Enjo, K.3    Obinata, M.4    Nukiwa, T.5    Ikawa, S.6
  • 27
    • 33750584813 scopus 로고    scopus 로고
    • Epigenetic regulation of x-linked cancer/ germline antigen genes by dnmt1 and dnmt3b
    • James SR, Link PA, Karpf AR. 2006. Epigenetic regulation of X-linked cancer/ germline antigen genes by DNMT1 and DNMT3b. Oncogene 25: 6975-6985.
    • (2006) Oncogene , vol.25 , pp. 6975-6985
    • James, S.R.1    Link, P.A.2    Karpf, A.R.3
  • 28
    • 77954362183 scopus 로고    scopus 로고
    • Examination of the specificity of dna methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine
    • Jin S-G, Kadam S, Pfeifer GP. 2010. Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine. Nucleic Acids Res 38: e125.
    • (2010) Nucleic Acids Res , vol.38
    • Jin, S.-G.1    Kadam, S.2    Pfeifer, G.P.3
  • 33
    • 77249137168 scopus 로고    scopus 로고
    • Principles and challenges of genomewide dna methylation analysis
    • Laird PW. 2010. Principles and challenges of genomewide DNA methylation analysis. Nat Rev Genet 11: 191-203.
    • (2010) Nat Rev Genet , vol.11 , pp. 191-203
    • Laird, P.W.1
  • 35
    • 79953177468 scopus 로고    scopus 로고
    • Aligning short sequencing reads with bowtie
    • Langmead B. 2010. Aligning short sequencing reads with Bowtie. Curr Protoc Bioinformatics 32: 111-117.
    • (2010) Curr Protoc Bioinformatics , vol.32 , pp. 111-117
    • Langmead, B.1
  • 37
    • 0036856355 scopus 로고    scopus 로고
    • Methprimer: Designing primers for methylation pcrs
    • Li LC, Dahiya R. 2002. MethPrimer: designing primers for methylation PCRs. Bioinformatics 18: 1427-1431.
    • (2002) Bioinformatics , vol.18 , pp. 1427-1431
    • Li, L.C.1    Dahiya, R.2
  • 38
    • 77949587649 scopus 로고    scopus 로고
    • Fast and accurate long-read alignment with burrows-wheeler transform
    • Li H, Durbin R. 2010. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26: 589-595.
    • (2010) Bioinformatics , vol.26 , pp. 589-595
    • Li, H.1    Durbin, R.2
  • 40
    • 80055010534 scopus 로고    scopus 로고
    • Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals
    • Lynch VJ, Leclerc RD, May G, Wagner GP. 2011. Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals. Nat Genet 43: 1154-1159.
    • (2011) Nat Genet , vol.43 , pp. 1154-1159
    • Lynch, V.J.1    Leclerc, R.D.2    May, G.3    Wagner, G.P.4
  • 48
    • 33746610114 scopus 로고    scopus 로고
    • Mage - A tumor antigens target p53 transactivation function through histone deacetylase recruitment and confer resistance to chemotherapeutic agents
    • Monte M, Simonatto M, Peche LY, Bublik DR, Gobessi S, Pierotti MA, Rodolfo M, Schneider C. 2006. MAGE-A tumor antigens target p53 transactivation function through histone deacetylase recruitment and confer resistance to chemotherapeutic agents. Proc Natl Acad Sci 103: 11160-11165.
    • (2006) Proc Natl Acad Sci , vol.103 , pp. 11160-11165
    • Monte, M.1    Simonatto, M.2    Peche, L.Y.3    Bublik, D.R.4    Gobessi, S.5    Pierotti, M.A.6    Rodolfo, M.7    Schneider, C.8
  • 54
    • 33846057724 scopus 로고    scopus 로고
    • Ncbi reference sequences (refseq): A curated non-redundant sequence database of genomes, transcripts and proteins
    • Pruitt KD, Tatusova T, Maglott DR. 2007. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 35: D61-D65.
    • (2007) Nucleic Acids Res , vol.35
    • Pruitt, K.D.1    Tatusova, T.2    Maglott, D.R.3
  • 56
    • 79958822224 scopus 로고    scopus 로고
    • Inhibition of histone lysine methylation enhances cancer-testis antigen expression in lung cancer cells: Implications for adoptive immunotherapy of cancer
    • Rao M, Chinnasamy N, Hong JA, Zhang Y, Zhang M, Xi S, Liu F, Marquez VE, Morgan RA, Schrump DS. 2011. Inhibition of histone lysine methylation enhances cancer-testis antigen expression in lung cancer cells: implications for adoptive immunotherapy of cancer. Cancer Res 71: 4192-4204.
    • (2011) Cancer Res , vol.71 , pp. 4192-4204
    • Rao, M.1    Chinnasamy, N.2    Hong, J.A.3    Zhang, Y.4    Zhang, M.5    Xi, S.6    Liu, F.7    Marquez, V.E.8    Morgan, R.A.9    Schrump, D.S.10
  • 57
  • 58
    • 77951850381 scopus 로고    scopus 로고
    • Bisma-fast and accurate bisulfite sequencing data analysis of individual clones from unique and repetitive sequences
    • Rohde C, Zhang Y, Reinhardt R, Jeltsch A. 2010. BISMA-fast and accurate bisulfite sequencing data analysis of individual clones from unique and repetitive sequences. BMC Bioinformatics 11: 230.
    • (2010) BMC Bioinformatics , vol.11 , pp. 230
    • Rohde, C.1    Zhang, Y.2    Reinhardt, R.3    Jeltsch, A.4
  • 63
    • 0031010342 scopus 로고    scopus 로고
    • A survey of telomerase activity in human cancer
    • Shay JW, Bacchetti S. 1997. A survey of telomerase activity in human cancer. Eur J Cancer 33: 787-791.
    • (1997) Eur J Cancer , vol.33 , pp. 787-791
    • Shay, J.W.1    Bacchetti, S.2
  • 64
    • 84866240316 scopus 로고    scopus 로고
    • Change-point model on nonhomogeneous poisson processes with application in copy number profiling by nextgeneration dna sequencing
    • Shen JJ, Zhang NR. 2012. Change-point model on nonhomogeneous Poisson processes with application in copy number profiling by nextgeneration DNA sequencing. Ann Appl Stat 6: 476-496.
    • (2012) Ann Appl Stat , vol.6 , pp. 476-496
    • Shen, J.J.1    Zhang, N.R.2
  • 66
    • 34147104969 scopus 로고    scopus 로고
    • A faster circular binary segmentation algorithm for the analysis of array cgh data
    • Venkatraman ES, Olshen AB. 2007. A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics 23: 657-663.
    • (2007) Bioinformatics , vol.23 , pp. 657-663
    • Venkatraman, E.S.1    Olshen, A.B.2
  • 67
    • 73649123907 scopus 로고    scopus 로고
    • Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in pdgfra, idh1, egfr, and nf1
    • Verhaak RG, Hoadley KA, Purdom E, Wang V, Qi Y, Wilkerson MD, Miller CR, Ding L, Golub T, Mesirov JP, et al. 2010. Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell 17: 98-110.
    • (2010) Cancer Cell , vol.17 , pp. 98-110
    • Verhaak, R.G.1    Hoadley, K.A.2    Purdom, E.3    Wang, V.4    Qi, Y.5    Wilkerson, M.D.6    Miller, C.R.7    Ding, L.8    Golub, T.9    Mesirov, J.P.10
  • 69
    • 34047116826 scopus 로고    scopus 로고
    • Distribution, silencing potential and evolutionary impact of promoterdnamethylation in the human genome
    • Weber M, Hellmann I, Stadler MB, Ramos L, Paabo S, Rebhan M, Schubeler D. 2007. Distribution, silencing potential and evolutionary impact of promoterDNAmethylation in the human genome. NatGenet 39: 457-466.
    • (2007) NatGenet , vol.39 , pp. 457-466
    • Weber, M.1    Hellmann, I.2    Stadler, M.B.3    Ramos, L.4    Paabo, S.5    Rebhan, M.6    Schubeler, D.7
  • 71
    • 77955700020 scopus 로고    scopus 로고
    • Genome-wide hypomethylation in cancer may be a passive consequence of transformation
    • Wild L, Flanagan JM. 2010.Genome-wide hypomethylation in cancer may be a passive consequence of transformation. Biochim Biophys Acta 1806: 50-57.
    • (2010) Biochim Biophys Acta , vol.1806 , pp. 50-57
    • Wild, L.1    Flanagan, J.M.2
  • 75
    • 84879611157 scopus 로고    scopus 로고
    • Dna hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape
    • Xie M, Hong C, Zhang B, Lowdon RF, Xing X, Li D, Zhou X, Lee HJ, Maire CL, Ligon KL, et al. 2013. DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape. Nat Genet 45: 836-841.
    • (2013) Nat Genet , vol.45 , pp. 836-841
    • Xie, M.1    Hong, C.2    Zhang, B.3    Lowdon, R.F.4    Xing, X.5    Li, D.6    Zhou, X.7    Lee, H.J.8    Maire, C.L.9    Ligon, K.L.10
  • 78
    • 84883668746 scopus 로고    scopus 로고
    • Functional dna methylation differences between tissues, cell types, and across individuals discovered using the m and m algorithm
    • Zhang B, Zhou Y, Lin N, Lowdon RF, Hong C, Nagarajan RP, Cheng JB, Li D, Stevens M, Lee HJ, et al. 2013. Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M and M algorithm. Genome Res 23: 1522-1540.
    • (2013) Genome Res , vol.23 , pp. 1522-1540
    • Zhang, B.1    Zhou, Y.2    Lin, N.3    Lowdon, R.F.4    Hong, C.5    Nagarajan, R.P.6    Cheng, J.B.7    Li, D.8    Stevens, M.9    Lee, H.J.10


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.