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Volumn 19, Issue 3, 2011, Pages 307-312

Tumour-specific methylation of PTPRG intron 1 locus in sporadic and Lynch syndrome colorectal cancer

Author keywords

colorectal cancer; CTCF; DNA methylation; Lynch syndrome; PTPRG

Indexed keywords

PROTEIN TYROSINE PHOSPHATASE; PROTEIN TYROSINE PHOSPHATASE GAMMA; TRANSCRIPTION FACTOR CTCF; UNCLASSIFIED DRUG;

EID: 79951814625     PISSN: 10184813     EISSN: 14765438     Source Type: Journal    
DOI: 10.1038/ejhg.2010.187     Document Type: Article
Times cited : (18)

References (42)
  • 1
    • 53049087109 scopus 로고    scopus 로고
    • Genomic and epigenetic instability in colorectal cancer pathogenesis
    • Grady WM, Carethers JM: Genomic and epigenetic instability in colorectal cancer pathogenesis. Gastroenterology 2008; 135: 1079-1099.
    • (2008) Gastroenterology , vol.135 , pp. 1079-1099
    • Grady, W.M.1    Carethers, J.M.2
  • 4
    • 33845643047 scopus 로고    scopus 로고
    • MMASS: An optimized array-based method for assessing CpG island methylation
    • Ibrahim AE, Thorne NP, Baird K et al: MMASS: an optimized array-based method for assessing CpG island methylation. Nucleic Acids Res 2006; 34: e136.
    • (2006) Nucleic Acids Res , vol.34
    • Ibrahim, A.E.1    Thorne, N.P.2    Baird, K.3
  • 5
    • 0033047813 scopus 로고    scopus 로고
    • Methylation profiling of CpG islands in human breast cancer cells
    • Huang TH, Perry MR, Laux DE: Methylation profiling of CpG islands in human breast cancer cells. Hum Mol Genet 1999; 8: 459-470. (Pubitemid 29097334)
    • (1999) Human Molecular Genetics , vol.8 , Issue.3 , pp. 459-470
    • Huang, T.H.-M.1    Perry, M.R.2    Laux, D.E.3
  • 7
    • 23044514626 scopus 로고    scopus 로고
    • Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells
    • DOI 10.1038/ng1598
    • Weber M, Davies JJ, Wittig D et al: Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 2005; 37: 853-862. (Pubitemid 41077111)
    • (2005) Nature Genetics , vol.37 , Issue.8 , pp. 853-862
    • Weber, M.1    Davies, J.J.2    Wittig, D.3    Oakeley, E.J.4    Haase, M.5    Lam, W.L.6    Schubeler, D.7
  • 9
    • 0036613250 scopus 로고    scopus 로고
    • A genomic screen for genes upregulated by demethylation and histone deacetylase inhibition in human colorectal cancer
    • Suzuki H, Gabrielson E, Chen W et al: A genomic screen for genes upregulated by demethylation and histone deacetylase inhibition in human colorectal cancer. Nat Genet 2002; 31: 141-149.
    • (2002) Nat Genet , vol.31 , pp. 141-149
    • Suzuki, H.1    Gabrielson, E.2    Chen, W.3
  • 11
    • 49649125042 scopus 로고    scopus 로고
    • Genome-scale DNA methylation maps of pluripotent and differentiated cells
    • Meissner A, Mikkelsen TS, Gu H et al: Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 2008; 454: 766-770.
    • (2008) Nature , vol.454 , pp. 766-770
    • Meissner, A.1    Mikkelsen, T.S.2    Gu, H.3
  • 12
    • 59149084538 scopus 로고    scopus 로고
    • The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores
    • Irizarry RA, Ladd-Acosta C, Wen B et al: The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet 2009; 41: 178-186.
    • (2009) Nat Genet , vol.41 , pp. 178-186
    • Irizarry, R.A.1    Ladd-Acosta, C.2    Wen, B.3
  • 13
    • 34047116826 scopus 로고    scopus 로고
    • Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome
    • DOI 10.1038/ng1990, PII NG1990
    • Weber M, Hellmann I, Stadler MB et al: Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet 2007; 39: 457-466. (Pubitemid 46514772)
    • (2007) Nature Genetics , vol.39 , Issue.4 , 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
  • 15
    • 0028340280 scopus 로고
    • Purification of CpG islands using a methylated DNA binding column
    • DOI 10.1038/ng0394-236
    • Cross SH, Charlton JA, Nan X et al: Purification of CpG islands using a methylated DNA binding column. Nat Genet 1994; 6: 236-244. (Pubitemid 24188619)
    • (1994) Nature Genetics , vol.6 , Issue.3 , pp. 236-244
    • Cross, S.H.1    Charlton, J.A.2    Nan, X.3    Bird, A.P.4
  • 16
    • 0028143269 scopus 로고
    • Analysis of changes in DNA sequence copy number by comparative genomic hybridization in archival paraffin-embedded tumor samples
    • Isola J, DeVries S, Chu L et al: Analysis of changes in DNA sequence copy number by comparative genomic hybridization in archival paraffin-embedded tumor samples. Am J Pathol 1994; 145: 1301-1308. (Pubitemid 24378485)
    • (1994) American Journal of Pathology , vol.145 , Issue.6 , pp. 1301-1308
    • Isola, J.1    DeVries, S.2    Chu, L.3    Ghazvini, S.4    Waldman, F.5
  • 17
    • 0036318071 scopus 로고    scopus 로고
    • Use of CpG island microarrays to identify colorectal tumors with a high degree of concurrent methylation
    • DOI 10.1016/S1046-2023(02)00070-1, PII S1046202302000701
    • Yan PS, Efferth T, Chen HL et al: Use of CpG island microarrays to identify colorectal tumors with a high degree of concurrent methylation. Methods 2002; 27: 162-169. (Pubitemid 34757129)
    • (2002) Methods , vol.27 , Issue.2 , pp. 162-169
    • Yan, P.S.1    Efferth, T.2    Chen, H.-L.3    Lin, J.4    Rodel, F.5    Fuzesi, L.6    Huang, T.H.-M.7
  • 19
    • 0001677717 scopus 로고
    • Controlling the false discovery rate - A practical and powerful approach to multiple testing
    • Benjamini Y, Hochberg Y: Controlling the false discovery rate - a practical and powerful approach to multiple testing. J R Stat Soc S B-Methodol 1995; 57: 289-300.
    • (1995) J R Stat Soc S B-Methodol , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 20
    • 0036856355 scopus 로고    scopus 로고
    • MethPrimer: Designing primers for methylation PCRs
    • Li LC, Dahiya R: MethPrimer: designing primers for methylation PCRs. Bioinformatics 2002; 18: 1427-1431. (Pubitemid 35414532)
    • (2002) Bioinformatics , vol.18 , Issue.11 , pp. 1427-1431
    • Li, L.-C.1    Dahiya, R.2
  • 22
    • 79951809804 scopus 로고    scopus 로고
    • Tom Hall
    • Tom Hall. BioEdit (URL: http://www.mbio.ncsu.edu/BioEdit/). 2008.
    • (2008) BioEdit
  • 23
    • 27744577751 scopus 로고    scopus 로고
    • BiQ Analyzer: Visualization and quality control for DNA methylation data from bisulfite sequencing
    • DOI 10.1093/bioinformatics/bti652
    • Bock C, Reither S, Mikeska T et al: BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing. Bioinformatics 2005; 21: 4067-4068. (Pubitemid 41631851)
    • (2005) Bioinformatics , vol.21 , Issue.21 , pp. 4067-4068
    • Bock, C.1    Reither, S.2    Mikeska, T.3    Paulsen, M.4    Walter, J.5    Lengauer, T.6
  • 24
    • 0033990048 scopus 로고    scopus 로고
    • Primer3 on the WWW for general users and for biologist programmers
    • Rozen S, Skaletsky H: Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 2000; 132: 365-386.
    • (2000) Methods Mol Biol , vol.132 , pp. 365-386
    • Rozen, S.1    Skaletsky, H.2
  • 25
    • 24044464247 scopus 로고    scopus 로고
    • Methylation-specific MLPA (MS-MLPA): Simultaneous detection of CpG methylation and copy number changes of up to 40 sequences
    • Nygren AO, Ameziane N, Duarte HM et al: Methylation-specific MLPA (MS-MLPA): simultaneous detection of CpG methylation and copy number changes of up to 40 sequences. Nucleic Acids Res 2005; 33: e128.
    • (2005) Nucleic Acids Res , vol.33
    • Nygren, A.O.1    Ameziane, N.2    Duarte, H.M.3
  • 26
    • 0037129827 scopus 로고    scopus 로고
    • Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes
    • RESEARCH0034
    • Vandesompele J, De PK, Pattyn F et al: Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 2002; 3: RESEARCH0034.
    • (2002) Genome Biol , pp. 3
    • Vandesompele, J.1    De Pk Pattyn, F.2
  • 30
    • 50249188284 scopus 로고    scopus 로고
    • Redundant DNA methylation in colorectal cancers of Lynch-syndrome patients
    • Alemayehu A, Sebova K, Fridrichova I: Redundant DNA methylation in colorectal cancers of Lynch-syndrome patients. Genes Chromosomes Cancer 2008; 47: 906-914.
    • (2008) Genes Chromosomes Cancer , vol.47 , pp. 906-914
    • Alemayehu, A.1    Sebova, K.2    Fridrichova, I.3
  • 33
    • 58149498240 scopus 로고    scopus 로고
    • CTCF-dependent enhancer-blocking by alternative chromatin loop formation
    • Hou C, Zhao H, Tanimoto K et al: CTCF-dependent enhancer-blocking by alternative chromatin loop formation. Proc Natl Acad Sci USA 2008; 105: 20398-20403.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 20398-20403
    • Hou, C.1    Zhao, H.2    Tanimoto, K.3
  • 34
    • 65549159993 scopus 로고    scopus 로고
    • Epigenetic silencing of the p16(INK4a) tumor suppressor is associated with loss of CTCF binding and a chromatin boundary
    • Witcher M, Emerson BM: Epigenetic silencing of the p16(INK4a) tumor suppressor is associated with loss of CTCF binding and a chromatin boundary. Mol Cell 2009; 34: 271-284.
    • (2009) Mol Cell , vol.34 , pp. 271-284
    • Witcher, M.1    Emerson, B.M.2
  • 35
    • 65649146793 scopus 로고    scopus 로고
    • Breaching the boundaries that safeguard against repression
    • Tiwari VK, Baylin SB: Breaching the boundaries that safeguard against repression. Mol Cell 2009; 34: 395-397.
    • (2009) Mol Cell , vol.34 , pp. 395-397
    • Tiwari, V.K.1    Baylin, S.B.2
  • 36
    • 34047245478 scopus 로고    scopus 로고
    • Epigenetic regulation of the human retinoblastoma tumor suppressor gene promoter by CTCF
    • DOI 10.1158/0008-5472.CAN-06-2024
    • De La Rosa-Velazquez IA, Rincon-Arano H, itez-Bribiesca L et al: Epigenetic regulation of the human retinoblastoma tumor suppressor gene promoter by CTCF. Cancer Res 2007; 67: 2577-2585. (Pubitemid 46548943)
    • (2007) Cancer Research , vol.67 , Issue.6 , pp. 2577-2585
    • De La Rosa-Velazquez, I.A.1    Rincon-Arano, H.2    Benitez-Bribiesca, L.3    Recillas-Targa, F.4
  • 37
    • 77950864281 scopus 로고    scopus 로고
    • CpG island methylation affects accessibility of the proximal BRCA1 promoter to transcription factors
    • Xu J, Huo D, Chen Y et al: CpG island methylation affects accessibility of the proximal BRCA1 promoter to transcription factors. Breast Cancer Res Treat 2009.
    • (2009) Breast Cancer Res Treat
    • Xu, J.1    Huo, D.2    Chen, Y.3
  • 38
    • 77956240630 scopus 로고    scopus 로고
    • DNA methylation prevents CTCF-mediated silencing of the oncogene BCL6 in B cell lymphomas
    • Lai AY, Fatemi M, Dhasarathy A et al: DNA methylation prevents CTCF-mediated silencing of the oncogene BCL6 in B cell lymphomas. J Exp Med 2010; 207: 1939-1950.
    • (2010) J Exp Med , vol.207 , pp. 1939-1950
    • Lai, A.Y.1    Fatemi, M.2    Dhasarathy, A.3
  • 40
    • 33745728166 scopus 로고    scopus 로고
    • Silencing of Peroxiredoxin 2 and aberrant methylation of 33 CpG islands in putative promoter regions in human malignant melanomas
    • Furuta J, Nobeyama Y, Umebayashi Y et al: Silencing of Peroxiredoxin 2 and aberrant methylation of 33 CpG islands in putative promoter regions in human malignant melanomas. Cancer Res 2006; 66: 6080-6086.
    • (2006) Cancer Res , vol.66 , pp. 6080-6086
    • Furuta, J.1    Nobeyama, Y.2    Umebayashi, Y.3
  • 41
    • 36248930484 scopus 로고    scopus 로고
    • Metastatic suppressor genes inactivated by aberrant methylation in gastric cancer
    • Wang JF, Dai DQ: Metastatic suppressor genes inactivated by aberrant methylation in gastric cancer. World J Gastroenterol 2007; 13: 5692-5698.
    • (2007) World J Gastroenterol , vol.13 , pp. 5692-5698
    • Wang, J.F.1    Dai, D.Q.2
  • 42
    • 1842715884 scopus 로고    scopus 로고
    • Genomic imprinting: CTCF protects the boundaries
    • DOI 10.1016/j.cub.2004.03.026, PII S0960982204001939
    • Lewis A, Murrell A: Genomic imprinting: CTCF protects the boundaries. Curr Biol 2004; 14: R284-R286. (Pubitemid 38458941)
    • (2004) Current Biology , vol.14 , Issue.7
    • Lewis, A.1    Murrell, A.2


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