메뉴 건너뛰기




Volumn , Issue 96, 2015, Pages

Targeted DNA methylation analysis by next-generation sequencing

Author keywords

Bioinformatics; CpG; Cytosine; DNA methylation; Epigenetics; Gene expression; Gene expression regulation; Issue 96; Molecular biology; Next generation sequencing

Indexed keywords

DNA; HYDROGEN SULFITE; SULFITE;

EID: 84946161473     PISSN: 1940087X     EISSN: None     Source Type: Journal    
DOI: 10.3791/52488     Document Type: Article
Times cited : (80)

References (24)
  • 1
    • 84957846754 scopus 로고
    • The quantitative separation of purines, pyrimidines, and nucleosides by paper chromatography
    • Hotchkiss, R. D. The quantitative separation of purines, pyrimidines, and nucleosides by paper chromatography. The Journal of Biological Chemistry. 175 (1), 315-332 (1948).
    • (1948) The Journal of Biological Chemistry , vol.175 , Issue.1 , pp. 315-332
    • Hotchkiss, R.D.1
  • 2
    • 0036144048 scopus 로고    scopus 로고
    • DNA methylation patterns and epigenetic memory
    • Bird, A. DNA methylation patterns and epigenetic memory. Genes & Development. 16 (1), 6-21, doi: 10.1101/gad.947102. (2002)
    • (2002) Genes & Development , vol.16 , Issue.1 , pp. 6-21
    • Bird, A.1
  • 3
    • 84874194072 scopus 로고    scopus 로고
    • DNA methylation: Roles in mammalian development. Nature reviews
    • Smith, Z. D., & Meissner, A. DNA methylation: roles in mammalian development. Nature reviews. Genetics. 14 (3), 204-220, doi: 10.1038/nrg3354. (2013)
    • (2013) Genetics , vol.14 , Issue.3 , pp. 204-220
    • Smith, Z.D.1    Meissner, A.2
  • 4
    • 84897139220 scopus 로고    scopus 로고
    • Transgenerational epigenetic inheritance: Myths and mechanisms
    • Heard, E., & Martienssen, R. A. Transgenerational epigenetic inheritance: myths and mechanisms. Cell. 157 (1), 95-109, doi: 10.1016/j.cell.2014.02.045. (2014)
    • (2014) Cell , vol.157 , Issue.1 , pp. 95-109
    • Heard, E.1    Martienssen, R.A.2
  • 5
    • 31344466008 scopus 로고    scopus 로고
    • DNA methylation and gene silencing in cancer
    • Baylin, S. B. DNA methylation and gene silencing in cancer. Nature Clinical Practice. Oncology. 2 Suppl 1, S4-11, doi: 10.1038/ncponc0354. (2005)
    • (2005) Oncology , vol.2 , Issue.1 , pp. S4-S11
    • Baylin, S.B.1
  • 6
    • 84862622426 scopus 로고    scopus 로고
    • The cancer epigenome: Its origins, contributions to tumorigenesis, and translational implications
    • Baylin, S. B. The cancer epigenome: its origins, contributions to tumorigenesis, and translational implications. Proceedings of the American Thoracic Society. 9 (2), 64-65, doi: 10.1513/pats.201201-001MS. (2012)
    • (2012) Proceedings of the American Thoracic Society , vol.9 , Issue.2 , pp. 64-65
    • Baylin, S.B.1
  • 7
    • 42649089780 scopus 로고    scopus 로고
    • The methylome: Approaches for global DNA methylation profiling
    • Beck, S., & Rakyan, V. K. The methylome: approaches for global DNA methylation profiling. Trends in Genetics: TIG. 24 (5), 231-237, doi: 10.1016/j.tig.2008.01.006. (2008)
    • (2008) Trends in Genetics: TIG , vol.24 , Issue.5 , pp. 231-237
    • Beck, S.1    Rakyan, V.K.2
  • 8
    • 77249137168 scopus 로고    scopus 로고
    • Principles and challenges of genomewide DNA methylation analysis
    • Laird, P. W. Principles and challenges of genomewide DNA methylation analysis. Nature reviews. Genetics. 11 (3), 191-203, doi: 10.1038/nrg2732. (2010)
    • (2010) Nature Reviews. Genetics , vol.11 , Issue.3 , pp. 191-203
    • Laird, P.W.1
  • 9
    • 34548147443 scopus 로고    scopus 로고
    • Optimization of quantitative MGMT promoter methylation analysis using pyrosequencing and combined bisulfite restriction analysis
    • Mikeska, T. et al. Optimization of quantitative MGMT promoter methylation analysis using pyrosequencing and combined bisulfite restriction analysis. The Journal of Molecular Diagnostics: JMD. 9(3), 368-381, doi: 10.2353/jmoldx.2007.060167. (2007)
    • (2007) The Journal of Molecular Diagnostics: JMD , vol.9 , Issue.3 , pp. 368-381
    • Mikeska, T.1
  • 11
    • 33947262084 scopus 로고    scopus 로고
    • Quantification of the methylation status of the PWS/AS imprinted region: Comparison of two approaches based on bisulfite sequencing and methylation-sensitive MLPA
    • Dikow, N. et al. Quantification of the methylation status of the PWS/AS imprinted region: comparison of two approaches based on bisulfite sequencing and methylation-sensitive MLPA. Molecular And Cellular Probes. 21 (3), 208-215, doi: 10.1016/j.mcp.2006.12.002. (2007)
    • (2007) Molecular and Cellular Probes , vol.21 , Issue.3 , pp. 208-215
    • Dikow, N.1
  • 12
    • 84868087624 scopus 로고    scopus 로고
    • Direct bisulfite sequencing for examination of DNA methylation with gene and nucleotide resolution from brain tissues
    • Jacqueline N. Crawley. [et al.]. Chapter 7
    • Parrish, R. R., Day, J. J., & Lubin, F. D. Direct bisulfite sequencing for examination of DNA methylation with gene and nucleotide resolution from brain tissues. Current Protocols In Neuroscience/editorial board, Jacqueline N. Crawley. [et al.]. Chapter 7, Unit 7 24, doi: 10.1002/0471142301.ns0724s60. (2012)
    • (2012) Current Protocols in Neuroscience/Editorial Board , vol.7
    • Parrish, R.R.1    Day, J.J.2    Lubin, F.D.3
  • 13
    • 33947297430 scopus 로고
    • Reactions of uracil and cytosine derivatives with sodium bisulfite. A specific deamination method
    • Shapiro, R., Servis, R.E. and Welcher, M. Reactions of uracil and cytosine derivatives with sodium bisulfite. A specific deamination method. Journal of the American Chemical Society. 92, 422-424 (1970).
    • (1970) Journal of the American Chemical Society , vol.92 , pp. 422-424
    • Shapiro, R.1    Servis, R.E.2    Welcher, M.3
  • 15
    • 0019332015 scopus 로고
    • Comparison of bisulfite modification of 5-methyldeoxycytidine and deoxycytidine residues
    • Wang, R. Y., Gehrke, C. W., & Ehrlich, M. Comparison of bisulfite modification of 5-methyldeoxycytidine and deoxycytidine residues. Nucleic Acids Research. 8 (20), 4777-4790 (1980).
    • (1980) Nucleic Acids Research , vol.8 , Issue.20 , pp. 4777-4790
    • Wang, R.Y.1    Gehrke, C.W.2    Ehrlich, M.3
  • 16
    • 84885368581 scopus 로고    scopus 로고
    • Focused, high accuracy 5-methylcytosine quantitation with base resolution by benchtop next-generation sequencing
    • Masser, D. R., Berg, A. S., & Freeman, W. M. Focused, high accuracy 5-methylcytosine quantitation with base resolution by benchtop next-generation sequencing. Epigenetics & Chromatin. 6 (1), 33, doi: 10.1186/1756-8935-6-33. (2013)
    • (2013) Epigenetics & Chromatin , vol.6 , Issue.1 , pp. 33
    • Masser, D.R.1    Berg, A.S.2    Freeman, W.M.3
  • 17
    • 79960070912 scopus 로고    scopus 로고
    • Preparation of next-generation sequencing libraries using Nextera technology: Simultaneous DNA fragmentation and adaptor tagging by in vitro transposition
    • Caruccio, N. Preparation of next-generation sequencing libraries using Nextera technology: simultaneous DNA fragmentation and adaptor tagging by in vitro transposition. Methods in Molecular Biology. 733, 241-255, doi: 10.1007/978-1-61779-089-8_17. (2011)
    • (2011) Methods in Molecular Biology , vol.733 , pp. 241-255
    • Caruccio, N.1
  • 18
    • 84865591846 scopus 로고    scopus 로고
    • A tale of three next generation sequencing platforms: Comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers
    • Quail, M. A. et al. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics. 13, 341, doi: 10.1186/1471-2164-13-341. (2012)
    • (2012) BMC Genomics , vol.13 , pp. 341
    • Quail, M.A.1
  • 19
    • 84861904633 scopus 로고    scopus 로고
    • Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing
    • Adey, A., & Shendure, J. Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing. Genome Research. 22 (6), 1139-1143, doi: 10.1101/gr.136242.111. (2012)
    • (2012) Genome Research , vol.22 , Issue.6 , pp. 1139-1143
    • Adey, A.1    Shendure, J.2
  • 20
    • 84905405443 scopus 로고    scopus 로고
    • Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity
    • Smallwood, S. A. et al. Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity. Nature Methods. 11 (8), 817-820, doi: 10.1038/nmeth.3035. (2014)
    • (2014) Nature Methods , vol.11 , Issue.8 , pp. 817-820
    • Smallwood, S.A.1
  • 21
    • 82455168223 scopus 로고    scopus 로고
    • Universal endogenous gene controls for bisulphite conversion in analysis of plant DNA methylation
    • Wang, J. et al. Universal endogenous gene controls for bisulphite conversion in analysis of plant DNA methylation. Plant Methods. 7, 39, doi: 10.1186/1746-4811-7-39. (2011)
    • (2011) Plant Methods , vol.7
    • Wang, J.1
  • 22
    • 70450217879 scopus 로고    scopus 로고
    • Human DNA methylomes at base resolution show widespread epigenomic differences
    • Lister, R. et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature. 462 (7271), 315-322, doi: 10.1038/nature08514. (2009)
    • (2009) Nature , vol.462 , Issue.7271 , pp. 315-322
    • Lister, R.1
  • 23
    • 84876042374 scopus 로고    scopus 로고
    • In-solution hybrid capture of bisulfite-converted DNA for targeted bisulfite sequencing of 174 ADME genes
    • Ivanov, M. et al. In-solution hybrid capture of bisulfite-converted DNA for targeted bisulfite sequencing of 174 ADME genes. Nucleic Acids Research. 41 (6), e72, doi: 10.1093/nar/gks1467. (2013)
    • (2013) Nucleic Acids Research , vol.41 , Issue.6
    • Ivanov, M.1
  • 24
    • 84885012678 scopus 로고    scopus 로고
    • Oxidative bisulfite sequencing of 5-methylcytosine and 5-hydroxymethylcytosine
    • Booth, M. J. et al. Oxidative bisulfite sequencing of 5-methylcytosine and 5-hydroxymethylcytosine. Nature Protocols. 8 (10), 1841-1851, doi: 10.1038/nprot.2013.115. (2013)
    • (2013) Nature Protocols , vol.8 , Issue.10 , pp. 1841-1851
    • Booth, M.J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.