메뉴 건너뛰기




Volumn 16, Issue 3, 2014, Pages 175-184

Methylated DNA immunoprecipitation and high-throughput sequencing (MeDIP-seq) using low amounts of genomic DNA

Author keywords

[No Author keywords available]

Indexed keywords

5 HYDROXYMETHYLCYTOSINE; 5 METHYLCYTOSINE; CYTOSINE; GENOMIC DNA; OCTAMER TRANSCRIPTION FACTOR 4; STAT3 PROTEIN; TRANSCRIPTION FACTOR NANOG; TRANSCRIPTION FACTOR SOX2; DNA; PRIMER DNA;

EID: 84901337843     PISSN: 21524971     EISSN: 21524998     Source Type: Journal    
DOI: 10.1089/cell.2014.0002     Document Type: Article
Times cited : (48)

References (35)
  • 1
    • 84861904633 scopus 로고    scopus 로고
    • Ultra-low-input, tagmentationbased whole-genome bisulfite sequencing
    • Adey, A., and Shendure, J. (2012). Ultra-low-input, tagmentationbased whole-genome bisulfite sequencing. Genome Res. 22, 1139-1143.
    • (2012) Genome Res. , vol.22 , pp. 1139-1143
    • Adey, A.1    Shendure, J.2
  • 2
    • 0028907753 scopus 로고
    • Embryonic stem cells express neuronal properties in vitro
    • Bain, G., Kitchens, D., Yao, M., Huettner, J.E., and Gottlieb, D.I. (1995). Embryonic stem cells express neuronal properties in vitro. Dev. Biol. 168, 342-357.
    • (1995) Dev. Biol. , vol.168 , pp. 342-357
    • Bain, G.1    Kitchens, D.2    Yao, M.3    Huettner, J.E.4    Gottlieb, D.I.5
  • 4
    • 80053144962 scopus 로고    scopus 로고
    • A decade of exploring the cancer epigenome - Biological and translational implications
    • Baylin, S.B., and Jones, P.A. (2011). A decade of exploring the cancer epigenome - biological and translational implications. Nat. Rev. Cancer 11, 726-734.
    • (2011) Nat. Rev. Cancer. , vol.11 , pp. 726-734
    • Baylin, S.B.1    Jones, P.A.2
  • 6
    • 84861221693 scopus 로고    scopus 로고
    • Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution
    • Booth, M.J., Branco, M.R., Ficz, G., Oxley, D., Krueger, F., Reik, W., and Balasubramanian, S. (2012). Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution. Science 336, 934-937.
    • (2012) Science , vol.336 , pp. 934-937
    • Booth, M.J.1    Branco, M.R.2    Ficz, G.3    Oxley, D.4    Krueger, F.5    Reik, W.6    Balasubramanian, S.7
  • 8
    • 84867548134 scopus 로고    scopus 로고
    • Methylated DNA immunoprecipitation (MeDIP) from low amounts of cells
    • Borgel, J., Guibert, S., and Weber, M. (2012). Methylated DNA immunoprecipitation (MeDIP) from low amounts of cells. Methods Mol. Biol. 925, 149-158.
    • (2012) Methods Mol. Biol. , vol.925 , pp. 149-158
    • Borgel, J.1    Guibert, S.2    Weber, M.3
  • 9
    • 79956330964 scopus 로고    scopus 로고
    • CpG islands and the regulation of transcription
    • Deaton, A.M., and Bird, A. (2011). CpG islands and the regulation of transcription. Genes Dev. 25, 1010-1022.
    • (2011) Genes Dev. , vol.25 , pp. 1010-1022
    • Deaton, A.M.1    Bird, A.2
  • 11
    • 38649126918 scopus 로고    scopus 로고
    • Promoter CpG Methylation Contributes to ES Cell Gene Regulation in Parallel with Oct4/Nanog, PcG Complex, and Histone H3 K4/K27 Trimethylation
    • DOI 10.1016/j.stem.2007.12.011, PII S193459090700327X
    • Fouse, S.D., Shen, Y., Pellegrini, M., Cole, S., Meissner, A., Van Neste, L., Jaenisch, R., and Fan, G. (2008). Promoter CpG methylation contributes to ES cell gene regulation in parallel with Oct4/Nanog, PcG complex, and histone H3 K4/K27 trimethylation. Cell Stem Cell 2, 160-169. (Pubitemid 351168712)
    • (2008) Cell Stem Cell , vol.2 , Issue.2 , pp. 160-169
    • Fouse, S.D.1    Shen, Y.2    Pellegrini, M.3    Cole, S.4    Meissner, A.5    Van Neste, L.6    Jaenisch, R.7    Fan, G.8
  • 12
    • 84869139022 scopus 로고    scopus 로고
    • Offspring from oocytes derived from in vitro primordial germ cell-like cells in mice
    • Hayashi, K., Ogushi, S., Kurimoto, K., Shimamoto, S., Ohta, H., and Saitou, M. (2012). Offspring from oocytes derived from in vitro primordial germ cell-like cells in mice. Science 338, 971-975.
    • (2012) Science , vol.338 , pp. 971-975
    • Hayashi, K.1    Ogushi, S.2    Kurimoto, K.3    Shimamoto, S.4    Ohta, H.5    Saitou, M.6
  • 14
    • 77956189495 scopus 로고    scopus 로고
    • Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification
    • Ito, S., D'Alessio, A.C., Taranova, O.V., Hong, K., Sowers, L.C., and Zhang, Y. (2010). Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification. Nature 466, 1129-1133.
    • (2010) Nature , vol.466 , pp. 1129-1133
    • Ito, S.1    D'Alessio, A.C.2    Taranova, O.V.3    Hong, K.4    Sowers, L.C.5    Zhang, Y.6
  • 15
    • 39149130361 scopus 로고    scopus 로고
    • Stem Cells, the Molecular Circuitry of Pluripotency and Nuclear Reprogramming
    • DOI 10.1016/j.cell.2008.01.015, PII S0092867408001153
    • Jaenisch, R., and Young, R. (2008). Stem cells, the molecular circuitry of pluripotency and nuclear reprogramming. Cell 132, 567-582. (Pubitemid 351253686)
    • (2008) Cell , vol.132 , Issue.4 , pp. 567-582
    • Jaenisch, R.1    Young, R.2
  • 16
    • 84863986133 scopus 로고    scopus 로고
    • Functions of DNA methylation: Islands, start sites, gene bodies and beyond
    • Jones, P.A. (2012). Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat. Rev. Genet. 13, 484-492.
    • (2012) Nat. Rev. Genet. , vol.13 , pp. 484-492
    • Jones, P.A.1
  • 18
    • 77249137168 scopus 로고    scopus 로고
    • Principles and challenges of genomewide DNA methylation analysis
    • Laird, P.W. (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
  • 19
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead, B., and Salzberg, S.L. (2012). Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357-359.
    • (2012) Nat. Methods. , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 21
    • 0026708177 scopus 로고
    • Targeted mutation of the DNA methyltransferase gene results in embryonic lethality
    • Li, E., Bestor, T.H., and Jaenisch, R. (1992). Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69, 915-926.
    • (1992) Cell , vol.69 , pp. 915-926
    • Li, E.1    Bestor, T.H.2    Jaenisch, R.3
  • 22
    • 3042678219 scopus 로고    scopus 로고
    • Neural differentiation of mouse embryonic stem cells in vitro and after transplantation into eyes of mutant mice with rapid retinal degeneration
    • DOI 10.1016/j.brainres.2004.04.019, PII S0006899304005852
    • Meyer, J.S., Katz, M.L., Maruniak, J.A., and Kirk, M.D. (2004). Neural differentiation of mouse embryonic stem cells in vitro and after transplantation into eyes of mutant mice with rapid retinal degeneration. Brain Res. 1014, 131-144. (Pubitemid 38801502)
    • (2004) Brain Research , vol.1014 , Issue.1-2 , pp. 131-144
    • Meyer, J.S.1    Katz, M.L.2    Maruniak, J.A.3    Kirk, M.D.4
  • 24
    • 0033615717 scopus 로고    scopus 로고
    • DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development
    • DOI 10.1016/S0092-8674(00)81656-6
    • Okano, M., Bell, D.W., Haber, D.A., and Li, E. (1999). DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99, 247-257. (Pubitemid 29519904)
    • (1999) Cell , vol.99 , Issue.3 , pp. 247-257
    • Okano, M.1    Bell, D.W.2    Haber, D.A.3    Li, E.4
  • 25
    • 84878260646 scopus 로고    scopus 로고
    • TETonic shift: Biological roles of TET proteins in DNA demethylation and transcription
    • Pastor, W.A., Aravind, L., and Rao, A. (2013). TETonic shift: biological roles of TET proteins in DNA demethylation and transcription. Nat. Rev. Mol. Cell Biol. 14, 341-356.
    • (2013) Nat. Rev. Mol. Cell Biol. , vol.14 , pp. 341-356
    • Pastor, W.A.1    Aravind, L.2    Rao, A.3
  • 26
    • 84878839889 scopus 로고    scopus 로고
    • Laser capture microdissectionreduced representation bisulfite sequencing (LCM-RRBS)maps changes in DNA methylation associated with gonadectomyinduced adrenocortical neoplasia in the mouse
    • Schillebeeckx, M., Schrade, A., Lobs, A.K., Pihlajoki, M., Wilson, D.B., and Mitra, R.D. (2013). Laser capture microdissectionreduced representation bisulfite sequencing (LCM-RRBS)maps changes in DNA methylation associated with gonadectomyinduced adrenocortical neoplasia in the mouse. Nucleic Acids Res. 41, e116.
    • (2013) Nucleic Acids Res. , vol.41
    • Schillebeeckx, M.1    Schrade, A.2    Lobs, A.K.3    Pihlajoki, M.4    Wilson, D.B.5    Mitra, R.D.6
  • 27
    • 84876946045 scopus 로고    scopus 로고
    • Genome-wide analysis reveals TET- and TDG-dependent 5-methylcytosine oxidation dynamics
    • Shen, L., Wu, H., Diep, D., Yamaguchi, S., D'Alessio, A.C., Fung, H.L., Zhang, K., and Zhang, Y. (2013). Genome-wide analysis reveals TET- and TDG-dependent 5-methylcytosine oxidation dynamics. Cell 153, 692-706.
    • (2013) Cell , vol.153 , pp. 692-706
    • Shen, L.1    Wu, H.2    Diep, D.3    Yamaguchi, S.4    D'Alessio, A.C.5    Fung, H.L.6    Zhang, K.7    Zhang, Y.8
  • 29
    • 84874194072 scopus 로고    scopus 로고
    • DNA methylation: Roles in mammalian development
    • Smith, Z.D., and Meissner, A. (2013). DNA methylation: Roles in mammalian development. Nat. Rev. Genet. 14, 204-220.
    • (2013) Nat. Rev. Genet. , vol.14 , pp. 204-220
    • Smith, Z.D.1    Meissner, A.2
  • 31
    • 0036311202 scopus 로고    scopus 로고
    • Identification and resolution of artifacts in bisulfite sequencing
    • DOI 10.1016/S1046-2023(02)00060-9, PII S1046202302000609
    • Warnecke, P.M., Stirzaker, C., Song, J., Grunau, C., Melki, J.R., and Clark, S.J. (2002). Identification and resolution of artifacts in bisulfite sequencing. Methods 27, 101-107. (Pubitemid 34757119)
    • (2002) Methods , vol.27 , Issue.2 , pp. 101-107
    • Warnecke, P.M.1    Stirzaker, C.2    Song, J.3    Grunau, C.4    Melki, J.R.5    Clark, S.J.6
  • 32
    • 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, J.J., Wittig, D., Oakeley, E.J., Haase, M., Lam, W.L., and Schubeler, D. (2005). Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat. Genet. 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
  • 33
    • 79954457998 scopus 로고    scopus 로고
    • Genome-wide analysis of 5- hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells
    • Wu, H., D'Alessio, A.C., Ito, S., Wang, Z., Cui, K., Zhao, K., Sun, Y.E., and Zhang, Y. (2011). Genome-wide analysis of 5- hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells. Genes Dev. 25, 679-684.
    • (2011) Genes Dev. , vol.25 , pp. 679-684
    • Wu, H.1    D'Alessio, A.C.2    Ito, S.3    Wang, Z.4    Cui, K.5    Zhao, K.6    Sun, Y.E.7    Zhang, Y.8
  • 34
    • 0030694713 scopus 로고    scopus 로고
    • Imprinted expression of the Igf2r gene depends on an intronic CpG island
    • DOI 10.1038/39631
    • Wutz, A., Smrzka, O.W., Schweifer, N., Schellander, K., Wagner, E.F., and Barlow, D.P. (1997). Imprinted expression of the Igf2r gene depends on an intronic CpG island. Nature 389, 745-749. (Pubitemid 27458963)
    • (1997) Nature , vol.389 , Issue.6652 , pp. 745-749
    • Wutz, A.1    Smrzka, O.W.2    Schweifer, N.3    Schellander, K.4    Wagner, E.F.5    Barlow, D.P.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.