메뉴 건너뛰기




Volumn 13, Issue 7, 2014, Pages 721-731

Methyl CpG Binding Domain Ultra-Sequencing: A novel method for identifying inter-individual and cell-type-specific variation in DNA methylation

Author keywords

DNA methylation; Genome wide; MBD; NeuN; Neuron; Next generation sequencing

Indexed keywords

5 METHYLCYTOSINE; GENOMIC DNA; SPACER DNA;

EID: 84907875259     PISSN: 16011848     EISSN: 1601183X     Source Type: Journal    
DOI: 10.1111/gbb.12150     Document Type: Article
Times cited : (22)

References (59)
  • 4
    • 84862640477 scopus 로고    scopus 로고
    • Maternal deprivation in rats is associated with corticotropin releasing hormone (Crh) promoter hypomethylation and enhances Crh transcriptional responses to stress in adulthood
    • Chen, J., Evans, A.N., Liu, Y., Honda, M., Saavedra, J.M. & Aguilera, G. (2012) Maternal deprivation in rats is associated with corticotropin releasing hormone (Crh) promoter hypomethylation and enhances Crh transcriptional responses to stress in adulthood. J Neuroendocrinol 24, 1055-1064.
    • (2012) J Neuroendocrinol , vol.24 , pp. 1055-1064
    • Chen, J.1    Evans, A.N.2    Liu, Y.3    Honda, M.4    Saavedra, J.M.5    Aguilera, G.6
  • 5
    • 84867539515 scopus 로고    scopus 로고
    • Epigenetic control of alternative mRNA processing at the imprinted Herc3/Nap1l5 locus
    • Cowley, M., Wood, A.J., Bohm, S., Schulz, R. & Oakey, R.J. (2012) Epigenetic control of alternative mRNA processing at the imprinted Herc3/Nap1l5 locus. Nucleic Acids Res 40, 8917-8926.
    • (2012) Nucleic Acids Res , vol.40 , pp. 8917-8926
    • Cowley, M.1    Wood, A.J.2    Bohm, S.3    Schulz, R.4    Oakey, R.J.5
  • 10
    • 79952788617 scopus 로고    scopus 로고
    • Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling
    • Gu, H., Smith, Z.D., Bock, C., Boyle, P., Gnirke, A. & Meissner, A. (2011) Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling. Nat Protoc 6, 468-481.
    • (2011) Nat Protoc , vol.6 , pp. 468-481
    • Gu, H.1    Smith, Z.D.2    Bock, C.3    Boyle, P.4    Gnirke, A.5    Meissner, A.6
  • 12
    • 84875700729 scopus 로고    scopus 로고
    • A cell epigenotype specific model for the correction of brain cellular heterogeneity bias and its application to age, brain region and major depression
    • Guintivano, J., Aryee, M.J. & Kaminsky, Z.A. (2013) A cell epigenotype specific model for the correction of brain cellular heterogeneity bias and its application to age, brain region and major depression. Epigenetics 8, 290-302.
    • (2013) Epigenetics , vol.8 , pp. 290-302
    • Guintivano, J.1    Aryee, M.J.2    Kaminsky, Z.A.3
  • 15
    • 84858681550 scopus 로고    scopus 로고
    • Commentary: the seven plagues of epigenetic epidemiology
    • Heijmans, B.T. & Mill, J. (2012) Commentary: the seven plagues of epigenetic epidemiology. Int J Epidemiol 41, 74-78.
    • (2012) Int J Epidemiol , vol.41 , pp. 74-78
    • Heijmans, B.T.1    Mill, J.2
  • 16
    • 84861547680 scopus 로고    scopus 로고
    • Evidence that microglia mediate the neurobiological effects of chronic psychological stress on the medial prefrontal cortex
    • Hinwood, M., Morandini, J., Day, T.A. & Walker, F.R. (2012) Evidence that microglia mediate the neurobiological effects of chronic psychological stress on the medial prefrontal cortex. Cereb Cortex 22, 1442-1454.
    • (2012) Cereb Cortex , vol.22 , pp. 1442-1454
    • Hinwood, M.1    Morandini, J.2    Day, T.A.3    Walker, F.R.4
  • 17
    • 79955557706 scopus 로고    scopus 로고
    • Neurons show distinctive DNA methylation profile and higher interindividual variations compared with non-neurons
    • Iwamoto, K., Bundo, M., Ueda, J., Oldham, M.C., Ukai, W., Hashimoto, E., Saito, T., Geschwind, D.H. & Kato, T. (2011) Neurons show distinctive DNA methylation profile and higher interindividual variations compared with non-neurons. Genome Res 21, 688-696.
    • (2011) Genome Res , vol.21 , pp. 688-696
    • Iwamoto, K.1    Bundo, M.2    Ueda, J.3    Oldham, M.C.4    Ukai, W.5    Hashimoto, E.6    Saito, T.7    Geschwind, D.H.8    Kato, T.9
  • 24
    • 84880011207 scopus 로고    scopus 로고
    • Long-lasting alterations to DNA methylation and ncRNAs could underlie the effects of fetal alcohol exposure in mice
    • Laufer, B.I., Mantha, K., Kleiber, M.L., Diehl, E.J., Addison, S.M. & Singh, S.M. (2013) Long-lasting alterations to DNA methylation and ncRNAs could underlie the effects of fetal alcohol exposure in mice. Dis Model Mech 6, 977-992.
    • (2013) Dis Model Mech , vol.6 , pp. 977-992
    • Laufer, B.I.1    Mantha, K.2    Kleiber, M.L.3    Diehl, E.J.4    Addison, S.M.5    Singh, S.M.6
  • 25
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li, H. & Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 28
    • 84879663784 scopus 로고    scopus 로고
    • Global epigenomic reconfiguration during mammalian brain development
    • Lister, R., Mukamel, E.A., Nery, J.R. et al. (2013) Global epigenomic reconfiguration during mammalian brain development. Science 341, 1237905.
    • (2013) Science , vol.341 , pp. 1237905
    • Lister, R.1    Mukamel, E.A.2    Nery, J.R.3
  • 29
    • 33344470365 scopus 로고    scopus 로고
    • FACS-array profiling of striatal projection neuron subtypes in juvenile and adult mouse brains
    • Lobo, M.K., Karsten, S.L., Gray, M., Geschwind, D.H. & Yang, X.W. (2006) FACS-array profiling of striatal projection neuron subtypes in juvenile and adult mouse brains. Nat Neurosci 9, 443-452.
    • (2006) Nat Neurosci , vol.9 , pp. 443-452
    • Lobo, M.K.1    Karsten, S.L.2    Gray, M.3    Geschwind, D.H.4    Yang, X.W.5
  • 30
    • 84875221641 scopus 로고    scopus 로고
    • Epigenetic modifications of GABAergic interneurons are associated with the schizophrenia-like phenotype induced by prenatal stress in mice
    • Matrisciano, F., Tueting, P., Dalal, I., Kadriu, B., Grayson, D.R., Davis, J.M., Nicoletti, F. & Guidotti, A. (2013) Epigenetic modifications of GABAergic interneurons are associated with the schizophrenia-like phenotype induced by prenatal stress in mice. Neuropharmacology 68, 184-194.
    • (2013) Neuropharmacology , vol.68 , pp. 184-194
    • Matrisciano, F.1    Tueting, P.2    Dalal, I.3    Kadriu, B.4    Grayson, D.R.5    Davis, J.M.6    Nicoletti, F.7    Guidotti, A.8
  • 33
    • 33847614418 scopus 로고    scopus 로고
    • Covalent modification of DNA regulates memory formation
    • Miller, C.A. & Sweatt, J.D. (2007) Covalent modification of DNA regulates memory formation. Neuron 53, 857-869.
    • (2007) Neuron , vol.53 , pp. 857-869
    • Miller, C.A.1    Sweatt, J.D.2
  • 35
    • 84877111454 scopus 로고    scopus 로고
    • Widespread and extensive lengthening of 3′ UTRs in the mammalian brain
    • Miura, P., Shenker, S., Andreu-Agullo, C., Westholm, J.O. & Lai, E.C. (2013) Widespread and extensive lengthening of 3′ UTRs in the mammalian brain. Genome Res 23, 812-825.
    • (2013) Genome Res , vol.23 , pp. 812-825
    • Miura, P.1    Shenker, S.2    Andreu-Agullo, C.3    Westholm, J.O.4    Lai, E.C.5
  • 36
    • 84864127740 scopus 로고    scopus 로고
    • Long-lasting regulation of hippocampal Bdnf gene transcription after contextual fear conditioning
    • Mizuno, K., Dempster, E., Mill, J. & Giese, K.P. (2012) Long-lasting regulation of hippocampal Bdnf gene transcription after contextual fear conditioning. Genes Brain Behav 11, 651-659.
    • (2012) Genes Brain Behav , vol.11 , pp. 651-659
    • Mizuno, K.1    Dempster, E.2    Mill, J.3    Giese, K.P.4
  • 38
    • 77952240732 scopus 로고    scopus 로고
    • DNA methylation of the POMC gene promoter is associated with craving in alcohol dependence
    • Muschler, M.A., Hillemacher, T., Kraus, C., Kornhuber, J., Bleich, S. & Frieling, H. (2010) DNA methylation of the POMC gene promoter is associated with craving in alcohol dependence. J Neural Transm 117, 513-519.
    • (2010) J Neural Transm , vol.117 , pp. 513-519
    • Muschler, M.A.1    Hillemacher, T.2    Kraus, C.3    Kornhuber, J.4    Bleich, S.5    Frieling, H.6
  • 39
    • 78651251739 scopus 로고    scopus 로고
    • Comparison of methyl-DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain (MBD) protein capture for genome-wide DNA methylation analysis reveal CpG sequence coverage bias
    • Nair, S.S., Coolen, M.W., Stirzaker, C., Song, J.Z., Statham, A.L., Strbenac, D., Robinson, M.D. & Clark, S.J. (2011) Comparison of methyl-DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain (MBD) protein capture for genome-wide DNA methylation analysis reveal CpG sequence coverage bias. Epigenetics 6, 34-44.
    • (2011) Epigenetics , vol.6 , pp. 34-44
    • Nair, S.S.1    Coolen, M.W.2    Stirzaker, C.3    Song, J.Z.4    Statham, A.L.5    Strbenac, D.6    Robinson, M.D.7    Clark, S.J.8
  • 41
    • 84880492025 scopus 로고    scopus 로고
    • Differential gene body methylation and reduced expression of cell adhesion and neurotransmitter receptor genes in adverse maternal environment
    • Oh, J.E., Chambwe, N., Klein, S., Gal, J., Andrews, S., Gleason, G., Shaknovich, R., Melnick, A., Campagne, F. & Toth, M. (2013) Differential gene body methylation and reduced expression of cell adhesion and neurotransmitter receptor genes in adverse maternal environment. Transl Psychiatry 3, e218.
    • (2013) Transl Psychiatry , vol.3 , pp. e218
    • Oh, J.E.1    Chambwe, N.2    Klein, S.3    Gal, J.4    Andrews, S.5    Gleason, G.6    Shaknovich, R.7    Melnick, A.8    Campagne, F.9    Toth, M.10
  • 43
    • 0015697938 scopus 로고
    • Isolated removal of hypothalamic or other brain nuclei of the rat
    • Palkovits, M. (1973) Isolated removal of hypothalamic or other brain nuclei of the rat. Brain Res 59, 449-450.
    • (1973) Brain Res , vol.59 , pp. 449-450
    • Palkovits, M.1
  • 44
    • 78650058320 scopus 로고    scopus 로고
    • Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias, and copy number variation
    • Robinson, M.D., Stirzaker, C., Statham, A.L., Coolen, M.W., Song, J.Z., Nair, S.S., Strbenac, D., Speed, T.P. & Clark, S.J. (2010) Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias, and copy number variation. Genome Res 20, 1719-1729.
    • (2010) Genome Res , vol.20 , pp. 1719-1729
    • Robinson, M.D.1    Stirzaker, C.2    Statham, A.L.3    Coolen, M.W.4    Song, J.Z.5    Nair, S.S.6    Strbenac, D.7    Speed, T.P.8    Clark, S.J.9
  • 47
    • 84882452116 scopus 로고    scopus 로고
    • Intragenic epigenetic changes modulate NCAM alternative splicing in neuronal differentiation
    • Schor, I.E., Fiszbein, A., Petrillo, E. & Kornblihtt, A.R. (2013) Intragenic epigenetic changes modulate NCAM alternative splicing in neuronal differentiation. EMBO J 32, 2264-2274.
    • (2013) EMBO J , vol.32 , pp. 2264-2274
    • Schor, I.E.1    Fiszbein, A.2    Petrillo, E.3    Kornblihtt, A.R.4
  • 48
    • 84864277953 scopus 로고    scopus 로고
    • DNA methylation in the developing hippocampus and amygdala of anxiety-prone versus risk-taking rats
    • Simmons, R.K., Howard, J.L., Simpson, D.N., Akil, H. & Clinton, S.M. (2012) DNA methylation in the developing hippocampus and amygdala of anxiety-prone versus risk-taking rats. Dev Neurosci 34, 58-67.
    • (2012) Dev Neurosci , vol.34 , pp. 58-67
    • Simmons, R.K.1    Howard, J.L.2    Simpson, D.N.3    Akil, H.4    Clinton, S.M.5
  • 49
    • 84883719710 scopus 로고    scopus 로고
    • Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods
    • Stevens, M., Cheng, J.B., Li, D., Xie, M., Hong, C., Maire, C.L., Ligon, K.L., Hirst, M., Marra, M.A., Costello, J.F. & Wang, T. (2013) Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods. Genome Res 23, 1541-1553.
    • (2013) Genome Res , vol.23 , pp. 1541-1553
    • Stevens, M.1    Cheng, J.B.2    Li, D.3    Xie, M.4    Hong, C.5    Maire, C.L.6    Ligon, K.L.7    Hirst, M.8    Marra, M.A.9    Costello, J.F.10    Wang, T.11
  • 51
    • 84863341417 scopus 로고    scopus 로고
    • Reversal of cocaine-conditioned place preference through methyl supplementation in mice: altering global DNA methylation in the prefrontal cortex
    • Tian, W., Zhao, M., Li, M., Song, T., Zhang, M., Quan, L., Li, S. & Sun, Z.S. (2012) Reversal of cocaine-conditioned place preference through methyl supplementation in mice: altering global DNA methylation in the prefrontal cortex. PLoS One 7, e33435.
    • (2012) PLoS One , vol.7 , pp. e33435
    • Tian, W.1    Zhao, M.2    Li, M.3    Song, T.4    Zhang, M.5    Quan, L.6    Li, S.7    Sun, Z.S.8
  • 52
    • 84874952864 scopus 로고    scopus 로고
    • Enrichment-based DNA methylation analysis using next-generation sequencing: sample exclusion, estimating changes in global methylation, and the contribution of replicate lanes
    • Trimarchi, M.P., Murphy, M., Frankhouser, D., Rodriguez, B.A., Curfman, J., Marcucci, G., Yan, P. & Bundschuh, R. (2012) Enrichment-based DNA methylation analysis using next-generation sequencing: sample exclusion, estimating changes in global methylation, and the contribution of replicate lanes. BMC Genomics 13 (Suppl 8), S6.
    • (2012) BMC Genomics , vol.13 , pp. S6
    • Trimarchi, M.P.1    Murphy, M.2    Frankhouser, D.3    Rodriguez, B.A.4    Curfman, J.5    Marcucci, G.6    Yan, P.7    Bundschuh, R.8
  • 53
    • 21544470472 scopus 로고
    • Brain DNA methylation as an index of genome participation in mechanisms of individually acquired memory
    • Vanyushi, B.F., Tushmalo, N.A. & Guskova, L.V. (1974) Brain DNA methylation as an index of genome participation in mechanisms of individually acquired memory. Dok Akad Nauk SSSR 219, 742-744.
    • (1974) Dok Akad Nauk SSSR , vol.219 , pp. 742-744
    • Vanyushi, B.F.1    Tushmalo, N.A.2    Guskova, L.V.3
  • 54
    • 0036708169 scopus 로고    scopus 로고
    • Analysis of neuronal gene expression with laser capture microdissection
    • Vincent, V.A., DeVoss, J.J., Ryan, H.S. & Murphy, G.M. Jr. (2002) Analysis of neuronal gene expression with laser capture microdissection. J Neurosci Res 69, 578-586.
    • (2002) J Neurosci Res , vol.69 , pp. 578-586
    • Vincent, V.A.1    DeVoss, J.J.2    Ryan, H.S.3    Murphy Jr, G.M.4
  • 55
    • 84881298161 scopus 로고    scopus 로고
    • Double restriction-enzyme digestion improves the coverage and accuracy of genome-wide CpG methylation profiling by reduced representation bisulfite sequencing
    • Wang, J., Xia, Y., Li, L., Gong, D., Yao, Y., Luo, H., Lu, H., Yi, N., Wu, H., Zhang, X., Tao, Q. & Gao, F. (2013) Double restriction-enzyme digestion improves the coverage and accuracy of genome-wide CpG methylation profiling by reduced representation bisulfite sequencing. BMC Genomics 14, 11.
    • (2013) BMC Genomics , vol.14 , pp. 11
    • Wang, J.1    Xia, Y.2    Li, L.3    Gong, D.4    Yao, Y.5    Luo, H.6    Lu, H.7    Yi, N.8    Wu, H.9    Zhang, X.10    Tao, Q.11    Gao, F.12
  • 56
    • 0030697141 scopus 로고    scopus 로고
    • Detection and measurement of PCR bias in quantitative methylation analysis of bisulphite-treated DNA
    • Warnecke, P.M., Stirzaker, C., Melki, J.R., Millar, D.S., Paul, C.L. & Clark, S.J. (1997) Detection and measurement of PCR bias in quantitative methylation analysis of bisulphite-treated DNA. Nucleic Acids Res 25, 4422-4426.
    • (1997) Nucleic Acids Res , vol.25 , pp. 4422-4426
    • Warnecke, P.M.1    Stirzaker, C.2    Melki, J.R.3    Millar, D.S.4    Paul, C.L.5    Clark, S.J.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.