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Volumn 5, Issue 1, 2016, Pages

DNA methylation analysis: Choosing the right method

Author keywords

5 methylcytosine; CpG islands; DNA methylation; Epigenetics; Next generation sequencing

Indexed keywords


EID: 84954460266     PISSN: None     EISSN: 20797737     Source Type: Journal    
DOI: 10.3390/biology5010003     Document Type: Review
Times cited : (513)

References (97)
  • 1
    • 84887129061 scopus 로고    scopus 로고
    • Strategies for discovery and validation of methylated and hydroxymethylated DNA biomarkers
    • [CrossRef] [PubMed]
    • Olkhov-Mitsel, E.; Bapat, B. Strategies for discovery and validation of methylated and hydroxymethylated DNA biomarkers. Cancer Med. 2012, 1, 237-260. [CrossRef] [PubMed]
    • (2012) Cancer Med , vol.1 , pp. 237-260
    • Olkhov-Mitsel, E.1    Bapat, B.2
  • 2
    • 84866480278 scopus 로고    scopus 로고
    • DNA methylation screening and analysis
    • [PubMed]
    • Sant, K.E.; Nahar, M.S.; Dolinoy, D.C. DNA methylation screening and analysis. Methods Mol. Biol. 2012, 889, 385-406. [PubMed]
    • (2012) Methods Mol. Biol , vol.889 , pp. 385-406
    • Sant, K.E.1    Nahar, M.S.2    Dolinoy, D.C.3
  • 3
    • 84908548564 scopus 로고    scopus 로고
    • Detection of DNA methylation by medip and mbdcap assays: An overview of techniques
    • [PubMed]
    • Hsu, H.K.; Weng, Y.I.; Hsu, P.Y.; Huang, T.H.; Huang, Y.W. Detection of DNA methylation by medip and mbdcap assays: An overview of techniques. Methods Mol. Biol. 2014, 1105, 61-70. [PubMed]
    • (2014) Methods Mol. Biol , vol.1105 , pp. 61-70
    • Hsu, H.K.1    Weng, Y.I.2    Hsu, P.Y.3    Huang, T.H.4    Huang, Y.W.5
  • 4
    • 84885447189 scopus 로고    scopus 로고
    • Optimizing methodologies for pcr-based DNA methylation analysis
    • [PubMed]
    • Hernandez, H.G.; Tse, M.Y.; Pang, S.C.; Arboleda, H.; Forero, D.A. Optimizing methodologies for pcr-based DNA methylation analysis. BioTechniques 2013, 55, 181-197. [PubMed]
    • (2013) BioTechniques , vol.55 , pp. 181-197
    • Hernandez, H.G.1    Tse, M.Y.2    Pang, S.C.3    Arboleda, H.4    Forero, D.A.5
  • 5
    • 84945206699 scopus 로고    scopus 로고
    • Base resolution methylome profiling: Considerations in platform selection, data preprocessing and analysis
    • [CrossRef] [PubMed]
    • Sun, Z.; Cunningham, J.; Slager, S.; Kocher, J.P. Base resolution methylome profiling: Considerations in platform selection, data preprocessing and analysis. Epigenomics 2015, 7, 813-828. [CrossRef] [PubMed]
    • (2015) Epigenomics , vol.7 , pp. 813-828
    • Sun, Z.1    Cunningham, J.2    Slager, S.3    Kocher, J.P.4
  • 6
    • 85042815231 scopus 로고    scopus 로고
    • (accessed on 20 December 2015)
    • Epigenie Informally Informative. Available online: http://epigenie.com/ (accessed on 20 December 2015).
    • Epigenie Informally Informative
  • 7
    • 77956389154 scopus 로고    scopus 로고
    • (accessed on 20 December 2015)
    • Protocol Online. Available online: http://www.protocol-online.org (accessed on 20 December 2015).
    • Protocol Online
  • 8
    • 84999530937 scopus 로고    scopus 로고
    • https://www.scienceexchange.com.
  • 10
    • 84999543261 scopus 로고    scopus 로고
    • Results from a healthy volunteer, single-dose, phase 1 study investigating the safety, tolerability, and pharmacokinetics of the nanobody (tm) alx-0081 targeting von willebrand factor
    • Klamroth, R.; Holz, J.B.; Vercruysse, K.; Dreier, T.; Silence, K.; Antoine, I.; Stanssens, P.; Berlin, P.P.T. Results from a healthy volunteer, single-dose, phase 1 study investigating the safety, tolerability, and pharmacokinetics of the nanobody (tm) alx-0081 targeting von willebrand factor. Arterioscl. Throm. Vas. 2008, 28, E72-E72.
    • (2008) Arterioscl. Throm. Vas , vol.28 , pp. E72-E72
    • Klamroth, R.1    Holz, J.B.2    Vercruysse, K.3    Dreier, T.4    Silence, K.5    Antoine, I.6    Stanssens, P.7    Berlin, P.P.T.8
  • 11
    • 84867208232 scopus 로고    scopus 로고
    • Association of polymorphisms in dnmt1, dnmt3a, dnmt3b, mthfr and mtrr genes with global DNA methylation levels and prognosis of autoimmune thyroid disease
    • [CrossRef] [PubMed]
    • Arakawa, Y.; Watanabe, M.; Inoue, N.; Sarumaru, M.; Hidaka, Y.; Iwatani, Y. Association of polymorphisms in dnmt1, dnmt3a, dnmt3b, mthfr and mtrr genes with global DNA methylation levels and prognosis of autoimmune thyroid disease. Clin. Exp. Immunol. 2012, 170, 194-201. [CrossRef] [PubMed]
    • (2012) Clin. Exp. Immunol , vol.170 , pp. 194-201
    • Arakawa, Y.1    Watanabe, M.2    Inoue, N.3    Sarumaru, M.4    Hidaka, Y.5    Iwatani, Y.6
  • 12
    • 84901018671 scopus 로고    scopus 로고
    • Epigenetic modification of nrf2 in 5-fluorouracil-resistant colon cancer cells: Involvement of tet-dependent DNA demethylation
    • [CrossRef] [PubMed]
    • Kang, K.A.; Piao, M.J.; Kim, K.C.; Kang, H.K.; Chang, W.Y.; Park, I.C.; Keum, Y.S.; Surh, Y.J.; Hyun, J.W. Epigenetic modification of nrf2 in 5-fluorouracil-resistant colon cancer cells: Involvement of tet-dependent DNA demethylation. Cell Death Dis. 2014, 5, e1183. [CrossRef] [PubMed]
    • (2014) Cell Death Dis , vol.5
    • Kang, K.A.1    Piao, M.J.2    Kim, K.C.3    Kang, H.K.4    Chang, W.Y.5    Park, I.C.6    Keum, Y.S.7    Surh, Y.J.8    Hyun, J.W.9
  • 16
    • 84904543823 scopus 로고    scopus 로고
    • High levels of global DNA methylation are an independent adverse prognostic factor in a series of 90 patients with de novo myelodysplastic syndrome
    • [CrossRef] [PubMed]
    • Calvo, X.; Nomdedeu, M.; Navarro, A.; Tejero, R.; Costa, D.; Munoz, C.; Pereira, A.; Pena, O.; Risueno, R.M.; Monzo, M.; et al. High levels of global DNA methylation are an independent adverse prognostic factor in a series of 90 patients with de novo myelodysplastic syndrome. Leuk. Res. 2014, 38, 874-881. [CrossRef] [PubMed]
    • (2014) Leuk. Res , vol.38 , pp. 874-881
    • Calvo, X.1    Nomdedeu, M.2    Navarro, A.3    Tejero, R.4    Costa, D.5    Munoz, C.6    Pereira, A.7    Pena, O.8    Risueno, R.M.9    Monzo, M.10
  • 17
    • 0019202657 scopus 로고
    • Quantitative reversed-phase high performance liquid chromatographic determination of major and modified deoxyribonucleosides in DNA
    • [CrossRef] [PubMed]
    • Kuo, K.C.; McCune, R.A.; Gehrke, C.W.; Midgett, R.; Ehrlich, M. Quantitative reversed-phase high performance liquid chromatographic determination of major and modified deoxyribonucleosides in DNA. Nucleic Acids Res. 1980, 8, 4763-4776. [CrossRef] [PubMed]
    • (1980) Nucleic Acids Res , vol.8 , pp. 4763-4776
    • Kuo, K.C.1    McCune, R.A.2    Gehrke, C.W.3    Midgett, R.4    Ehrlich, M.5
  • 18
    • 12244279345 scopus 로고    scopus 로고
    • Specific method for the determination of genomic DNA methylation by liquid chromatography-electrospray ionization tandem mass spectrometry
    • [CrossRef] [PubMed]
    • Song, L.; James, S.R.; Kazim, L.; Karpf, A.R. Specific method for the determination of genomic DNA methylation by liquid chromatography-electrospray ionization tandem mass spectrometry. Anal. Chem. 2005, 77, 504-510. [CrossRef] [PubMed]
    • (2005) Anal. Chem , vol.77 , pp. 504-510
    • Song, L.1    James, S.R.2    Kazim, L.3    Karpf, A.R.4
  • 19
    • 79953217366 scopus 로고    scopus 로고
    • A sensitive mass spectrometry method for simultaneous quantification of DNA methylation and hydroxymethylation levels in biological samples
    • Thuc, L.; Kim, K.P.; Fan, G.; Faull, K.F. A sensitive mass spectrometry method for simultaneous quantification of DNA methylation and hydroxymethylation levels in biological samples. Anal. Biochem. 2011, 412, 203-209.
    • (2011) Anal. Biochem , vol.412 , pp. 203-209
    • Thuc, L.1    Kim, K.P.2    Fan, G.3    Faull, K.F.4
  • 20
    • 67449155879 scopus 로고    scopus 로고
    • Quantification of regional DNA methylation by liquid chromatography/tandem mass spectrometry
    • [CrossRef] [PubMed]
    • Liu, Z.;Wu, J.; Xie, Z.; Liu, S.; Fan-Havard, P.; Huang, T.H.; Plass, C.; Marcucci, G.; Chan, K.K. Quantification of regional DNA methylation by liquid chromatography/tandem mass spectrometry. Anal. Biochem. 2009, 391, 106-113. [CrossRef] [PubMed]
    • (2009) Anal. Biochem , vol.391 , pp. 106-113
    • Liu, Z.1    Wu, J.2    Xie, Z.3    Liu, S.4    Fan-Havard, P.5    Huang, T.H.6    Plass, C.7    Marcucci, G.8    Chan, K.K.9
  • 21
    • 54549103517 scopus 로고    scopus 로고
    • DNA methylation determination by liquid chromatography-tandem mass spectrometry using novel biosynthetic [u-15n]deoxycytidine and [u-15n]methyldeoxycytidine internal standards
    • [CrossRef] [PubMed]
    • Quinlivan, E.P.; Gregory, J.F., 3rd. DNA methylation determination by liquid chromatography-tandem mass spectrometry using novel biosynthetic [u-15n]deoxycytidine and [u-15n]methyldeoxycytidine internal standards. Nucleic Acids Res. 2008, 36, e119. [CrossRef] [PubMed]
    • (2008) Nucleic Acids Res , vol.36
    • Quinlivan, E.P.1    Gregory, J.F.2
  • 22
    • 84900420062 scopus 로고    scopus 로고
    • Gene expression profile and toxic effects in human bronchial epithelial cells exposed to zearalenone
    • [CrossRef] [PubMed]
    • So, M.Y.; Tian, Z.; Phoon, Y.S.; Sha, S.; Antoniou, M.N.; Zhang, J.;Wu, R.S.; Tan-Un, K.C. Gene expression profile and toxic effects in human bronchial epithelial cells exposed to zearalenone. PLoS ONE 2014, 9, e96404. [CrossRef] [PubMed]
    • (2014) PLoS ONE , vol.9
    • So, M.Y.1    Tian, Z.2    Phoon, Y.S.3    Sha, S.4    Antoniou, M.N.5    Zhang, J.6    Wu, R.S.7    Tan-Un, K.C.8
  • 23
    • 79961151346 scopus 로고    scopus 로고
    • The global DNA methylation surrogate line-1 methylation is correlated with mgmt promoter methylation and is a better prognostic factor for glioma
    • [CrossRef] [PubMed]
    • Ohka, F.; Natsume, A.; Motomura, K.; Kishida, Y.; Kondo, Y.; Abe, T.; Nakasu, Y.; Namba, H.; Wakai, K.; Fukui, T.; et al. The global DNA methylation surrogate line-1 methylation is correlated with mgmt promoter methylation and is a better prognostic factor for glioma. PLoS ONE 2011, 6, e23332. [CrossRef] [PubMed]
    • (2011) PLoS ONE , vol.6
    • Ohka, F.1    Natsume, A.2    Motomura, K.3    Kishida, Y.4    Kondo, Y.5    Abe, T.6    Nakasu, Y.7    Namba, H.8    Wakai, K.9    Fukui, T.10
  • 26
    • 84890118277 scopus 로고    scopus 로고
    • Hypomethylation of long interspersed nuclear element-1 promoter is associated with poor outcomes for curative resected hepatocellular carcinoma
    • [CrossRef] [PubMed]
    • Gao, X.D.; Qu, J.H.; Chang, X.J.; Lu, Y.Y.; Bai,W.L.;Wang, H.; Xu, Z.X.; An, L.J.;Wang, C.P.; Zeng, Z.; et al. Hypomethylation of long interspersed nuclear element-1 promoter is associated with poor outcomes for curative resected hepatocellular carcinoma. Liver Int. 2014, 34, 136-146. [CrossRef] [PubMed]
    • (2014) Liver Int , vol.34 , pp. 136-146
    • Gao, X.D.1    Qu, J.H.2    Chang, X.J.3    Lu, Y.Y.4    Bai, W.L.5    Wang, H.6    Xu, Z.X.7    An, L.J.8    Wang, C.P.9    Zeng, Z.10
  • 27
    • 84895494085 scopus 로고    scopus 로고
    • Hypomethylation of long interspersed nuclear element-1 (line-1) leads to activation of proto-oncogenes in human colorectal cancer metastasis
    • [CrossRef] [PubMed]
    • Hur, K.; Cejas, P.; Feliu, J.; Moreno-Rubio, J.; Burgos, E.; Boland, C.R.; Goel, A. Hypomethylation of long interspersed nuclear element-1 (line-1) leads to activation of proto-oncogenes in human colorectal cancer metastasis. Gut 2014, 63, 635-646. [CrossRef] [PubMed]
    • (2014) Gut , vol.63 , pp. 635-646
    • Hur, K.1    Cejas, P.2    Feliu, J.3    Moreno-Rubio, J.4    Burgos, E.5    Boland, C.R.6    Goel, A.7
  • 28
    • 84940245895 scopus 로고    scopus 로고
    • Hypomethylation of long interspersed nuclear element-1 (line-1) is associated with poor prognosis via activation of c-met in hepatocellular carcinoma
    • [CrossRef] [PubMed]
    • Zhu, C.; Utsunomiya, T.; Ikemoto, T.; Yamada, S.; Morine, Y.; Imura, S.; Arakawa, Y.; Takasu, C.; Ishikawa, D.; Imoto, I.; et al. Hypomethylation of long interspersed nuclear element-1 (line-1) is associated with poor prognosis via activation of c-met in hepatocellular carcinoma. Ann. Surg. Oncol. 2014, 21, S729-S735. [CrossRef] [PubMed]
    • (2014) Ann. Surg. Oncol , vol.21 , pp. S729-S735
    • Zhu, C.1    Utsunomiya, T.2    Ikemoto, T.3    Yamada, S.4    Morine, Y.5    Imura, S.6    Arakawa, Y.7    Takasu, C.8    Ishikawa, D.9    Imoto, I.10
  • 30
    • 0036923869 scopus 로고    scopus 로고
    • Methylation-sensitive rflps: Characterisation of two oil palm markers showing somaclonal variation-associated polymorphism
    • [PubMed]
    • Jaligot, E.; Beule, T.; Rival, A. Methylation-sensitive rflps: Characterisation of two oil palm markers showing somaclonal variation-associated polymorphism. Theor. Appl. Genet. 2002, 104, 1263-1269. [PubMed]
    • (2002) Theor. Appl. Genet , vol.104 , pp. 1263-1269
    • Jaligot, E.1    Beule, T.2    Rival, A.3
  • 31
    • 61449514321 scopus 로고    scopus 로고
    • Analysis of DNA methylation by amplification of intermethylated sites (aims)
    • [PubMed]
    • Jorda, M.; Rodriguez, J.; Frigola, J.; Peinado, M.A. Analysis of DNA methylation by amplification of intermethylated sites (aims). Methods Mol. Biol. 2009, 507, 107-116. [PubMed]
    • (2009) Methods Mol. Biol , vol.507 , pp. 107-116
    • Jorda, M.1    Rodriguez, J.2    Frigola, J.3    Peinado, M.A.4
  • 32
    • 0034743280 scopus 로고    scopus 로고
    • Notl-msell methylation-sensitive amplied fragment length polymorhism for DNA methylation analysis of human cancers
    • [CrossRef]
    • Yamamoto, F.; Yamamoto, M.; Soto, J.L.; Kojima, E.; Wang, E.N.; Perucho, M.; Sekiya, T.; Yamanaka, H. Notl-msell methylation-sensitive amplied fragment length polymorhism for DNA methylation analysis of human cancers. Electrophoresis 2001, 22, 1946-1956. [CrossRef]
    • (2001) Electrophoresis , vol.22 , pp. 1946-1956
    • Yamamoto, F.1    Yamamoto, M.2    Soto, J.L.3    Kojima, E.4    Wang, E.N.5    Perucho, M.6    Sekiya, T.7    Yamanaka, H.8
  • 33
    • 0034558663 scopus 로고    scopus 로고
    • Aflp-based detection of DNA methylation
    • [CrossRef]
    • Xu, M.L.; Li, X.Q.; Korban, S.S. Aflp-based detection of DNA methylation. Plant Mol. Biol. Rep. 2000, 18, 361-368. [CrossRef]
    • (2000) Plant Mol. Biol. Rep , vol.18 , pp. 361-368
    • Xu, M.L.1    Li, X.Q.2    Korban, S.S.3
  • 37
    • 84941562055 scopus 로고    scopus 로고
    • Highly sensitive targeted methylome sequencing by post-bisulfite adaptor tagging
    • [CrossRef] [PubMed]
    • Miura, F.; Ito, T. Highly sensitive targeted methylome sequencing by post-bisulfite adaptor tagging. DNA Res. 2014, 22, 13-18. [CrossRef] [PubMed]
    • (2014) DNA Res , vol.22 , pp. 13-18
    • Miura, F.1    Ito, T.2
  • 38
    • 34247156577 scopus 로고    scopus 로고
    • Using luma a luminometric-based assay for global DNA-methylation
    • [PubMed]
    • Karimi, M.; Johansson, S.; Ekstrom, T.J. Using luma a luminometric-based assay for global DNA-methylation. Epigenetics 2006, 1, 45-48. [PubMed]
    • (2006) Epigenetics , vol.1 , pp. 45-48
    • Karimi, M.1    Johansson, S.2    Ekstrom, T.J.3
  • 42
    • 84877868707 scopus 로고    scopus 로고
    • Activation of bdnf signaling prevents the return of fear in female mice
    • [CrossRef] [PubMed]
    • Baker-Andresen, D.; Flavell, C.R.; Li, X.; Bredy, T.W. Activation of bdnf signaling prevents the return of fear in female mice. Learn. Mem. 2013, 20, 237-240. [CrossRef] [PubMed]
    • (2013) Learn. Mem , vol.20 , pp. 237-240
    • Baker-Andresen, D.1    Flavell, C.R.2    Li, X.3    Bredy, T.W.4
  • 43
    • 84883376375 scopus 로고    scopus 로고
    • Zac1 regulates astroglial differentiation of neural stem cells through socs3
    • [CrossRef] [PubMed]
    • Schmidt-Edelkraut, U.; Hoffmann, A.; Daniel, G.; Spengler, D. Zac1 regulates astroglial differentiation of neural stem cells through socs3. Stem Cells 2013, 31, 1621-1632. [CrossRef] [PubMed]
    • (2013) Stem Cells , vol.31 , pp. 1621-1632
    • Schmidt-Edelkraut, U.1    Hoffmann, A.2    Daniel, G.3    Spengler, D.4
  • 44
    • 84935039049 scopus 로고    scopus 로고
    • Epigenetic changes during hepatic stellate cell activation
    • [CrossRef] [PubMed]
    • Gotze, S.; Schumacher, E.C.; Kordes, C.; Haussinger, D. Epigenetic changes during hepatic stellate cell activation. PLoS ONE 2015, 10, e0128745. [CrossRef] [PubMed]
    • (2015) PLoS ONE , vol.10
    • Gotze, S.1    Schumacher, E.C.2    Kordes, C.3    Haussinger, D.4
  • 45
    • 84931274676 scopus 로고    scopus 로고
    • Characterization of functional methylomes by next-generation capture sequencing identifies novel disease-associated variants
    • [CrossRef] [PubMed]
    • Allum, F.; Shao, X.; Guenard, F.; Simon, M.M.; Busche, S.; Caron, M.; Lambourne, J.; Lessard, J.; Tandre, K.; Hedman, A.K.; et al. Characterization of functional methylomes by next-generation capture sequencing identifies novel disease-associated variants. Nat. Commun. 2015, 6, 7211. [CrossRef] [PubMed]
    • (2015) Nat. Commun , vol.6
    • Allum, F.1    Shao, X.2    Guenard, F.3    Simon, M.M.4    Busche, S.5    Caron, M.6    Lambourne, J.7    Lessard, J.8    Tandre, K.9    Hedman, A.K.10
  • 48
    • 84923848592 scopus 로고    scopus 로고
    • Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing
    • [CrossRef] [PubMed]
    • Ziller, M.J.; Hansen, K.D.; Meissner, A.; Aryee, M.J. Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing. Nat. Methods 2015, 12, 230-232. [CrossRef] [PubMed]
    • (2015) Nat. Methods , vol.12 , pp. 230-232
    • Ziller, M.J.1    Hansen, K.D.2    Meissner, A.3    Aryee, M.J.4
  • 49
    • 84868134071 scopus 로고    scopus 로고
    • Single nucleotide analysis of cytosine methylation by whole-genome shotgun bisulfite sequencing
    • [CrossRef]
    • Johnson, M.D.; Mueller, M.; Game, L.; Aitman, T.J. Single nucleotide analysis of cytosine methylation by whole-genome shotgun bisulfite sequencing. Curr. Protoc. Mol. Biol. 2012. [CrossRef]
    • (2012) Curr. Protoc. Mol. Biol
    • Johnson, M.D.1    Mueller, M.2    Game, L.3    Aitman, T.J.4
  • 50
    • 84892168013 scopus 로고    scopus 로고
    • Improved reduced representation bisulfite sequencing for epigenomic profiling of clinical samples
    • [CrossRef] [PubMed]
    • Lee, Y.K.; Jin, S.; Duan, S.; Lim, Y.C.; Ng, D.P.; Lin, X.M.; Yeo, G.; Ding, C. Improved reduced representation bisulfite sequencing for epigenomic profiling of clinical samples. Biol. Proced. Online 2014, 16, 1. [CrossRef] [PubMed]
    • (2014) Biol. Proced. Online , vol.16
    • Lee, Y.K.1    Jin, S.2    Duan, S.3    Lim, Y.C.4    Ng, D.P.5    Lin, X.M.6    Yeo, G.7    Ding, C.8
  • 51
    • 27144500218 scopus 로고    scopus 로고
    • Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis
    • [CrossRef] [PubMed]
    • Meissner, A.; Gnirke, A.; Bell, G.W.; Ramsahoye, B.; Lander, E.S.; Jaenisch, R. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res. 2005, 33, 5868-5877. [CrossRef] [PubMed]
    • (2005) Nucleic Acids Res , vol.33 , pp. 5868-5877
    • Meissner, A.1    Gnirke, A.2    Bell, G.W.3    Ramsahoye, B.4    Lander, E.S.5    Jaenisch, R.6
  • 52
    • 84899148704 scopus 로고    scopus 로고
    • DNA methylome profiling identifies novel methylated genes in african american patients with colorectal neoplasia
    • [CrossRef] [PubMed]
    • Ashktorab, H.; Daremipouran, M.; Goel, A.; Varma, S.; Leavitt, R.; Sun, X.; Brim, H. DNA methylome profiling identifies novel methylated genes in african american patients with colorectal neoplasia. Epigenetics 2014, 9, 503-512. [CrossRef] [PubMed]
    • (2014) Epigenetics , vol.9 , pp. 503-512
    • Ashktorab, H.1    Daremipouran, M.2    Goel, A.3    Varma, S.4    Leavitt, R.5    Sun, X.6    Brim, H.7
  • 54
    • 79959326644 scopus 로고    scopus 로고
    • Expanded methyl-sensitive cut counting reveals hypomethylation as an epigenetic state that highlights functional sequences of the genome
    • [CrossRef] [PubMed]
    • Colaneri, A.; Staffa, N.; Fargo, D.C.; Gao, Y.; Wang, T.Y.; Peddada, S.D.; Birnbaumer, L. Expanded methyl-sensitive cut counting reveals hypomethylation as an epigenetic state that highlights functional sequences of the genome. Proc. Natl. Acad. Sci. USA 2011, 108, 9715-9720. [CrossRef] [PubMed]
    • (2011) Proc. Natl. Acad. Sci. USA , vol.108 , pp. 9715-9720
    • Colaneri, A.1    Staffa, N.2    Fargo, D.C.3    Gao, Y.4    Wang, T.Y.5    Peddada, S.D.6    Birnbaumer, L.7
  • 55
    • 84875984010 scopus 로고    scopus 로고
    • Genome-wide quantitative identification of DNA differentially methylated sites in arabidopsis seedlings growing at different water potential
    • [CrossRef] [PubMed]
    • Colaneri, A.C.; Jones, A.M. Genome-wide quantitative identification of DNA differentially methylated sites in arabidopsis seedlings growing at different water potential. PLoS ONE 2013, 8. [CrossRef] [PubMed]
    • (2013) PLoS ONE
    • Colaneri, A.C.1    Jones, A.M.2
  • 56
    • 84863757162 scopus 로고    scopus 로고
    • Epigenetic modifications in frontal cortex from alzheimer's disease and bipolar disorder patients
    • [CrossRef] [PubMed]
    • Rao, J.S.; Keleshian, V.L.; Klein, S.; Rapoport, S.I. Epigenetic modifications in frontal cortex from alzheimer's disease and bipolar disorder patients. Transl. Psychiatry 2012, 2, e132. [CrossRef] [PubMed]
    • (2012) Transl. Psychiatry , vol.2
    • Rao, J.S.1    Keleshian, V.L.2    Klein, S.3    Rapoport, S.I.4
  • 58
    • 84869013266 scopus 로고    scopus 로고
    • Technical considerations for reduced representation bisulfite sequencing with multiplexed libraries
    • [CrossRef] [PubMed]
    • Chatterjee, A.; Rodger, E.J.; Stockwell, P.A.;Weeks, R.J.; Morison, I.M. Technical considerations for reduced representation bisulfite sequencing with multiplexed libraries. J. Biomed. Biotechnol. 2012, 2012, 741542. [CrossRef] [PubMed]
    • (2012) J. Biomed. Biotechnol , vol.2012
    • Chatterjee, A.1    Rodger, E.J.2    Stockwell, P.A.3    Weeks, R.J.4    Morison, I.M.5
  • 59
    • 84945238384 scopus 로고    scopus 로고
    • DNA methylation profiling: Comparison of genome-wide sequencing methods and the infinium human methylation 450 bead chip
    • [CrossRef] [PubMed]
    • Walker, D.L.; Bhagwate, A.V.; Baheti, S.; Smalley, R.L.; Hilker, C.A.; Sun, Z.; Cunningham, J.M. DNA methylation profiling: Comparison of genome-wide sequencing methods and the infinium human methylation 450 bead chip. Epigenomics 2015, 7, 1287-1302. [CrossRef] [PubMed]
    • (2015) Epigenomics , vol.7 , pp. 1287-1302
    • Walker, D.L.1    Bhagwate, A.V.2    Baheti, S.3    Smalley, R.L.4    Hilker, C.A.5    Sun, Z.6    Cunningham, J.M.7
  • 62
    • 84888101866 scopus 로고    scopus 로고
    • Error rates for nanopore discrimination among cytosine, methylcytosine, and hydroxymethylcytosine along individual DNA strands
    • [CrossRef] [PubMed]
    • Schreiber, J.; Wescoe, Z.L.; Abu-Shumays, R.; Vivian, J.T.; Baatar, B.; Karplus, K.; Akeson, M. Error rates for nanopore discrimination among cytosine, methylcytosine, and hydroxymethylcytosine along individual DNA strands. Proc. Natl. Acad. Sci. USA 2013, 110, 18910-18915. [CrossRef] [PubMed]
    • (2013) Proc. Natl. Acad. Sci. USA , vol.110 , pp. 18910-18915
    • Schreiber, J.1    Wescoe, Z.L.2    Abu-Shumays, R.3    Vivian, J.T.4    Baatar, B.5    Karplus, K.6    Akeson, M.7
  • 63
    • 61449477534 scopus 로고    scopus 로고
    • Goldengate assay for DNA methylation profiling
    • [PubMed]
    • Bibikova, M.; Fan, J.B. Goldengate assay for DNA methylation profiling. Methods Mol. Biol. 2009, 507, 149-163. [PubMed]
    • (2009) Methods Mol. Biol , vol.507 , pp. 149-163
    • Bibikova, M.1    Fan, J.B.2
  • 65
    • 84879092628 scopus 로고    scopus 로고
    • DNA methylation data analysis and its application to cancer research
    • [CrossRef] [PubMed]
    • Ma, X.; Wang, Y.W.; Zhang, M.Q.; Gazdar, A.F. DNA methylation data analysis and its application to cancer research. Epigenomics 2013, 5, 301-316. [CrossRef] [PubMed]
    • (2013) Epigenomics , vol.5 , pp. 301-316
    • Ma, X.1    Wang, Y.W.2    Zhang, M.Q.3    Gazdar, A.F.4
  • 66
    • 84871688621 scopus 로고    scopus 로고
    • Analysing and interpreting DNA methylation data
    • [CrossRef] [PubMed]
    • Bock, C. Analysing and interpreting DNA methylation data. Nat. Rev. Genet. 2012, 13, 705-719. [CrossRef] [PubMed]
    • (2012) Nat. Rev. Genet , vol.13 , pp. 705-719
    • Bock, C.1
  • 68
    • 34347217103 scopus 로고    scopus 로고
    • Methylation-specific digital karyotyping
    • [CrossRef] [PubMed]
    • Hu, M.; Yao, J.; Polyak, K. Methylation-specific digital karyotyping. Nat. Protoc. 2006, 1, 1621-1636. [CrossRef] [PubMed]
    • (2006) Nat. Protoc , vol.1 , pp. 1621-1636
    • Hu, M.1    Yao, J.2    Polyak, K.3
  • 69
    • 64349091471 scopus 로고    scopus 로고
    • Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells
    • [CrossRef] [PubMed]
    • Ball, M.P.; Li, J.B.; Gao, Y.; Lee, J.H.; LeProust, E.M.; Park, I.H.; Xie, B.; Daley, G.Q.; Church, G.M. Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat. Biotechnol. 2009, 27, 361-368. [CrossRef] [PubMed]
    • (2009) Nat. Biotechnol , vol.27 , pp. 361-368
    • Ball, M.P.1    Li, J.B.2    Gao, Y.3    Lee, J.H.4    LeProust, E.M.5    Park, I.H.6    Xie, B.7    Daley, G.Q.8    Church, G.M.9
  • 70
    • 77950527721 scopus 로고    scopus 로고
    • Optimized design and data analysis of tag-based cytosine methylation assays
    • [CrossRef] [PubMed]
    • Suzuki, M.; Jing, Q.; Lia, D.; Pascual, M.; McLellan, A.; Greally, J.M. Optimized design and data analysis of tag-based cytosine methylation assays. Genome Biol. 2010, 11, R36. [CrossRef] [PubMed]
    • (2010) Genome Biol , vol.11
    • Suzuki, M.1    Jing, Q.2    Lia, D.3    Pascual, M.4    McLellan, A.5    Greally, J.M.6
  • 73
    • 67649132826 scopus 로고    scopus 로고
    • An improved method for genome wide DNA methylation profiling correlated to transcription and genomic instability in two breast cancer cell lines
    • [CrossRef] [PubMed]
    • Li, J.; Gao, F.; Li, N.; Li, S.; Yin, G.; Tian, G.; Jia, S.; Wang, K.; Zhang, X.; Yang, H.; et al. An improved method for genome wide DNA methylation profiling correlated to transcription and genomic instability in two breast cancer cell lines. BMC Genom. 2009, 10, 223. [CrossRef] [PubMed]
    • (2009) BMC Genom , vol.10
    • Li, J.1    Gao, F.2    Li, N.3    Li, S.4    Yin, G.5    Tian, G.6    Jia, S.7    Wang, K.8    Zhang, X.9    Yang, H.10
  • 74
    • 39849085506 scopus 로고    scopus 로고
    • Substrate specificity of new methyl-directed DNA endonuclease glai
    • [CrossRef] [PubMed]
    • Tarasova, G.V.; Nayakshina, T.N.; Degtyarev, S.K. Substrate specificity of new methyl-directed DNA endonuclease glai. BMC Mol. Biol. 2008, 9, 7. [CrossRef] [PubMed]
    • (2008) BMC Mol. Biol , vol.9
    • Tarasova, G.V.1    Nayakshina, T.N.2    Degtyarev, S.K.3
  • 75
    • 84871790438 scopus 로고    scopus 로고
    • Sensitive and selective amplification of methylated DNA sequences using helper-dependent chain reaction in combination with a methylation-dependent restriction enzymes
    • [CrossRef] [PubMed]
    • Rand, K.N.; Young, G.P.; Ho, T.; Molloy, P.L. Sensitive and selective amplification of methylated DNA sequences using helper-dependent chain reaction in combination with a methylation-dependent restriction enzymes. Nucleic Acids Res. 2013, 41. [CrossRef] [PubMed]
    • (2013) Nucleic Acids Res
    • Rand, K.N.1    Young, G.P.2    Ho, T.3    Molloy, P.L.4
  • 77
    • 85042816431 scopus 로고    scopus 로고
    • (accessed on 20 December 2015)
    • High-Throughput DNA Methylation Profiling with VeraCode® Technology. Available online: http://www.illumina.com/content/dam/illumina-marketing/documents/products/datasheets/datasheet _veracode_methylation.pdf (accessed on 20 December 2015).
    • High-Throughput DNA Methylation Profiling with VeraCode® Technology.
  • 78
    • 84902990802 scopus 로고    scopus 로고
    • (accessed on 20 December 2015)
    • Methprimer. Available online: http://www.urogene.org/methprimer (accessed on 20 December 2015).
    • Methprimer.
  • 79
    • 84902734225 scopus 로고    scopus 로고
    • The 2ha line of medicago truncatula has characteristics of an epigenetic mutant that is weakly ethylene insensitive
    • [CrossRef] [PubMed]
    • Kurdyukov, S.; Mathesius, U.; Nolan, K.E.; Sheahan, M.B.; Goffard, N.; Carroll, B.J.; Rose, R.J. The 2ha line of medicago truncatula has characteristics of an epigenetic mutant that is weakly ethylene insensitive. Bmc Plant Biol. 2014, 14, 174. [CrossRef] [PubMed]
    • (2014) Bmc Plant Biol , vol.14
    • Kurdyukov, S.1    Mathesius, U.2    Nolan, K.E.3    Sheahan, M.B.4    Goffard, N.5    Carroll, B.J.6    Rose, R.J.7
  • 81
    • 0029843950 scopus 로고    scopus 로고
    • Methylation-specific pcr: A novel pcr assay for methylation status of cpg islands
    • [CrossRef] [PubMed]
    • Herman, J.G.; Graff, J.R.; Myohanen, S.; Nelkin, B.D.; Baylin, S.B. Methylation-specific pcr: A novel pcr assay for methylation status of cpg islands. Proc. Natl. Acad. Sci. USA 1996, 93, 9821-9826. [CrossRef] [PubMed]
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93 , pp. 9821-9826
    • Herman, J.G.1    Graff, J.R.2    Myohanen, S.3    Nelkin, B.D.4    Baylin, S.B.5
  • 82
    • 63349097282 scopus 로고    scopus 로고
    • Methylation-sensitive high-resolution melting
    • [CrossRef] [PubMed]
    • Wojdacz, T.K.; Dobrovic, A.; Hansen, L.L. Methylation-sensitive high-resolution melting. Nat. Protoc. 2008, 3, 1903-1908. [CrossRef] [PubMed]
    • (2008) Nat. Protoc , vol.3 , pp. 1903-1908
    • Wojdacz, T.K.1    Dobrovic, A.2    Hansen, L.L.3
  • 83
    • 84899618281 scopus 로고    scopus 로고
    • Cold-pcr amplification of bisulfite-converted DNA allows the enrichment and sequencing of rare un-methylated genomic regions
    • [CrossRef] [PubMed]
    • Castellanos-Rizaldos, E.; Milbury, C.A.; Karatza, E.; Chen, C.C.; Makrigiorgos, G.M.; Merewood, A. Cold-pcr amplification of bisulfite-converted DNA allows the enrichment and sequencing of rare un-methylated genomic regions. PLoS ONE 2014, 9, e94103. [CrossRef] [PubMed]
    • (2014) PLoS ONE , vol.9
    • Castellanos-Rizaldos, E.1    Milbury, C.A.2    Karatza, E.3    Chen, C.C.4    Makrigiorgos, G.M.5    Merewood, A.6
  • 84
    • 84857021124 scopus 로고    scopus 로고
    • The application of methylation specific electrophoresis (mse) to DNA methylation analysis of the 51 cpg island of mucin in cancer cells
    • [CrossRef] [PubMed]
    • Yokoyama, S.; Kitamoto, S.; Yamada, N.; Houjou, I.; Sugai, T.; Nakamura, S.; Arisaka, Y.; Takaori, K.; Higashi, M.; Yonezawa, S. The application of methylation specific electrophoresis (mse) to DNA methylation analysis of the 51 cpg island of mucin in cancer cells. BMC Cancer 2012, 12, 67. [CrossRef] [PubMed]
    • (2012) BMC Cancer , vol.12
    • Yokoyama, S.1    Kitamoto, S.2    Yamada, N.3    Houjou, I.4    Sugai, T.5    Nakamura, S.6    Arisaka, Y.7    Takaori, K.8    Higashi, M.9    Yonezawa, S.10
  • 85
    • 0018370141 scopus 로고
    • Direct detection of methylated cytosine in DNA by use of the restriction enzyme mspi
    • [CrossRef] [PubMed]
    • Cedar, H.; Solage, A.; Glaser, G.; Razin, A. Direct detection of methylated cytosine in DNA by use of the restriction enzyme mspi. Nucleic Acids Res. 1979, 6, 2125-2132. [CrossRef] [PubMed]
    • (1979) Nucleic Acids Res , vol.6 , pp. 2125-2132
    • Cedar, H.1    Solage, A.2    Glaser, G.3    Razin, A.4
  • 87
    • 84939644014 scopus 로고    scopus 로고
    • Mbridge: An accurate and cost-effective method for profiling DNA methylome at single-base resolution
    • [CrossRef] [PubMed]
    • Cai, W.; Mao, F.; Teng, H.; Cai, T.; Zhao, F.; Wu, J.; Sun, Z.S. Mbridge: An accurate and cost-effective method for profiling DNA methylome at single-base resolution. J. Mol. Cell Biol. 2015, 7, 299-313. [CrossRef] [PubMed]
    • (2015) J. Mol. Cell Biol , vol.7 , pp. 299-313
    • Cai, W.1    Mao, F.2    Teng, H.3    Cai, T.4    Zhao, F.5    Wu, J.6    Sun, Z.S.7
  • 88
    • 77957932941 scopus 로고    scopus 로고
    • Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications
    • [CrossRef] [PubMed]
    • Harris, R.A.; Wang, T.; Coarfa, C.; Nagarajan, R.P.; Hong, C.; Downey, S.L.; Johnson, B.E.; Fouse, S.D.; Delaney, A.; Zhao, Y.; et al. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat. Biotechnol. 2010, 28, 1097-1105. [CrossRef] [PubMed]
    • (2010) Nat. Biotechnol , vol.28 , pp. 1097-1105
    • Harris, R.A.1    Wang, T.2    Coarfa, C.3    Nagarajan, R.P.4    Hong, C.5    Downey, S.L.6    Johnson, B.E.7    Fouse, S.D.8    Delaney, A.9    Zhao, Y.10
  • 89
    • 27744443057 scopus 로고    scopus 로고
    • Methylated-cpg island recovery assay: A new technique for the rapid detection of methylated-cpg islands in cancer
    • [CrossRef] [PubMed]
    • Rauch, T.; Pfeifer, G.P. Methylated-cpg island recovery assay: A new technique for the rapid detection of methylated-cpg islands in cancer. Lab. Investig. 2005, 85, 1172-1180. [CrossRef] [PubMed]
    • (2005) Lab. Investig , vol.85 , pp. 1172-1180
    • Rauch, T.1    Pfeifer, G.P.2
  • 90
    • 84875290402 scopus 로고    scopus 로고
    • Genome-wide DNA methylation analysis using massively parallel sequencing technologies
    • [CrossRef] [PubMed]
    • Suzuki, M.; Greally, J.M. Genome-wide DNA methylation analysis using massively parallel sequencing technologies. Semin. Hematol. 2013, 50, 70-77. [CrossRef] [PubMed]
    • (2013) Semin. Hematol , vol.50 , pp. 70-77
    • Suzuki, M.1    Greally, J.M.2
  • 91
    • 67651149735 scopus 로고    scopus 로고
    • High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers
    • [CrossRef] [PubMed]
    • Oda, M.; Glass, J.L.; Thompson, R.F.; Mo, Y.; Olivier, E.N.; Figueroa, M.E.; Selzer, R.R.; Richmond, T.A.; Zhang, X.; Dannenberg, L.; et al. High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers. Nucleic Acids Res. 2009, 37, 3829-3839. [CrossRef] [PubMed]
    • (2009) Nucleic Acids Res , vol.37 , pp. 3829-3839
    • Oda, M.1    Glass, J.L.2    Thompson, R.F.3    Mo, Y.4    Olivier, E.N.5    Figueroa, M.E.6    Selzer, R.R.7    Richmond, T.A.8    Zhang, X.9    Dannenberg, L.10
  • 92
    • 65549107163 scopus 로고    scopus 로고
    • Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver
    • [CrossRef] [PubMed]
    • Brunner, A.L.; Johnson, D.S.; Kim, S.W.; Valouev, A.; Reddy, T.E.; Neff, N.F.; Anton, E.; Medina, C.; Nguyen, L.; Chiao, E.; et al. Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver. Genome Res. 2009, 19, 1044-1056. [CrossRef] [PubMed]
    • (2009) Genome Res , vol.19 , pp. 1044-1056
    • Brunner, A.L.1    Johnson, D.S.2    Kim, S.W.3    Valouev, A.4    Reddy, T.E.5    Neff, N.F.6    Anton, E.7    Medina, C.8    Nguyen, L.9    Chiao, E.10
  • 94
    • 35748959649 scopus 로고    scopus 로고
    • Microarray-based genomic selection for high-throughput resequencing
    • [CrossRef] [PubMed]
    • Okou, D.T.; Steinberg, K.M.; Middle, C.; Cutler, D.J.; Albert, T.J.; Zwick, M.E. Microarray-based genomic selection for high-throughput resequencing. Nat. Methods 2007, 4, 907-909. [CrossRef] [PubMed]
    • (2007) Nat. Methods , vol.4 , pp. 907-909
    • Okou, D.T.1    Steinberg, K.M.2    Middle, C.3    Cutler, D.J.4    Albert, T.J.5    Zwick, M.E.6
  • 95
    • 84862189441 scopus 로고    scopus 로고
    • The human oligogenome resource: A database of oligonucleotide capture probes for resequencing target regions across the human genome
    • [CrossRef] [PubMed]
    • Newburger, D.E.; Natsoulis, G.; Grimes, S.; Bell, J.M.; Davis, R.W.; Batzoglou, S.; Ji, H.P. The human oligogenome resource: A database of oligonucleotide capture probes for resequencing target regions across the human genome. Nucleic Acids Res. 2012, 40, D1137-D1143. [CrossRef] [PubMed]
    • (2012) Nucleic Acids Res , vol.40 , pp. D1137-D1143
    • Newburger, D.E.1    Natsoulis, G.2    Grimes, S.3    Bell, J.M.4    Davis, R.W.5    Batzoglou, S.6    Ji, H.P.7
  • 96
  • 97
    • 80054754790 scopus 로고    scopus 로고
    • Whole genome methylation scanning based on phi29 polymerase amplification
    • [CrossRef] [PubMed]
    • Brooks, R.; Rose, R.J.; Sheahan, M.B.; Kurdyukov, S. Whole genome methylation scanning based on phi29 polymerase amplification. Biochemistry 2011, 76, 999-1002. [CrossRef] [PubMed]
    • (2011) Biochemistry , vol.76 , pp. 999-1002
    • Brooks, R.1    Rose, R.J.2    Sheahan, M.B.3    Kurdyukov, S.4


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