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Volumn 6, Issue 1, 2013, Pages

A novel methyl-binding domain protein enrichment method for identifying genome-wide tissue-specific DNA methylation from nanogram DNA samples

Author keywords

DNA methylation; MBD; Nanogram; Retina; Tissue specific differentially methylated regions

Indexed keywords

BINDING PROTEIN; DNA; MACROGOL; METHYL BINDING DOMAIN PROTEIN; UNCLASSIFIED DRUG;

EID: 84878623709     PISSN: None     EISSN: 17568935     Source Type: Journal    
DOI: 10.1186/1756-8935-6-17     Document Type: Article
Times cited : (18)

References (32)
  • 1
    • 0026546877 scopus 로고
    • A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands
    • 10.1073/pnas.89.5.1827 1542678
    • A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Frommer M, McDonald LE, Millar DS, Collis CM, Watt F, Grigg GW, Molloy PL, Paul CL, Proc Natl Acad Sci USA 1992 89 1827 1831 10.1073/pnas.89.5.1827 1542678
    • (1992) Proc Natl Acad Sci USA , vol.89 , pp. 1827-1831
    • Frommer, M.1    McDonald, L.E.2    Millar, D.S.3    Collis, C.M.4    Watt, F.5    Grigg, G.W.6    Molloy, P.L.7    Paul, C.L.8
  • 5
    • 27744443057 scopus 로고    scopus 로고
    • Methylated-CpG island recovery assay: A new technique for the rapid detection of methylated-CpG islands in cancer
    • 10.1038/labinvest.3700311 16025148
    • Methylated-CpG island recovery assay: a new technique for the rapid detection of methylated-CpG islands in cancer. Rauch T, Pfeifer GP, Lab Invest 2005 85 1172 1180 10.1038/labinvest.3700311 16025148
    • (2005) Lab Invest , vol.85 , pp. 1172-1180
    • Rauch, T.1    Pfeifer, G.P.2
  • 6
    • 84866919003 scopus 로고    scopus 로고
    • Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging
    • 10.1093/nar/gks454 22649061
    • Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging. Miura F, Enomoto Y, Dairiki R, Ito T, Nucleic Acids Res 2012 40 136 10.1093/nar/gks454 22649061
    • (2012) Nucleic Acids Res , vol.40 , pp. 5136
    • Miura, F.1    Enomoto, Y.2    Dairiki, R.3    Ito, T.4
  • 7
    • 84861904633 scopus 로고    scopus 로고
    • Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing
    • 10.1101/gr.136242.111 22466172
    • Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing. Adey A, Shendure J, Genome Res 2012 22 1139 1143 10.1101/gr.136242.111 22466172
    • (2012) Genome Res , vol.22 , pp. 1139-1143
    • Adey, A.1    Shendure, J.2
  • 9
    • 79952788617 scopus 로고    scopus 로고
    • Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling
    • 10.1038/nprot.2010.190 21412275
    • Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling. Gu H, Smith ZD, Bock C, Boyle P, Gnirke A, Meissner A, Nat Protoc 2011 6 468 481 10.1038/nprot.2010.190 21412275
    • (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
  • 10
    • 77957932941 scopus 로고    scopus 로고
    • Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications
    • 10.1038/nbt.1682 20852635
    • Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, et al. Nat Biotechnol 2010 28 1097 1105 10.1038/nbt.1682 20852635
    • (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
  • 11
    • 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
    • 10.4161/epi.6.1.13313 20818161
    • 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 SS, Coolen MW, Stirzaker C, Song JZ, Statham AL, Strbenac D, Robinson MD, Clark SJ, Epigenetics 2011 6 34 44 10.4161/epi.6.1.13313 20818161
    • (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
  • 12
    • 77953253061 scopus 로고    scopus 로고
    • HELP (HpaII tiny fragment enrichment by ligation-mediated PCR) assay for DNA methylation profiling of primary normal and malignant B lymphocytes
    • 10.1007/978-1-60761-663-4-12 20217579
    • HELP (HpaII tiny fragment enrichment by ligation-mediated PCR) assay for DNA methylation profiling of primary normal and malignant B lymphocytes. Shaknovich R, Figueroa ME, Melnick A, Methods Mol Biol 2010 632 191 201 10.1007/978-1-60761-663-4-12 20217579
    • (2010) Methods Mol Biol , vol.632 , pp. 191-201
    • Shaknovich, R.1    Figueroa, M.E.2    Melnick, A.3
  • 16
    • 59149084538 scopus 로고    scopus 로고
    • The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores
    • 10.1038/ng.298 19151715
    • The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Irizarry RA, Ladd-Acosta C, Wen B, Wu Z, Montano C, Onyango P, Cui H, Gabo K, Rongione M, Webster M, et al. Nat Genet 2009 41 178 186 10.1038/ng.298 19151715
    • (2009) Nat Genet , vol.41 , pp. 178-186
    • Irizarry, R.A.1    Ladd-Acosta, C.2    Wen, B.3    Wu, Z.4    Montano, C.5    Onyango, P.6    Cui, H.7    Gabo, K.8    Rongione, M.9    Webster, M.10
  • 18
    • 0021112785 scopus 로고
    • Polymer-stimulated ligation: Enhanced blunt- or cohesive-end ligation of DNA or deoxyribooligonucleotides by T4 DNA ligase in polymer solutions
    • 10.1093/nar/11.22.7853 6359064
    • Polymer-stimulated ligation: enhanced blunt- or cohesive-end ligation of DNA or deoxyribooligonucleotides by T4 DNA ligase in polymer solutions. Pheiffer BH, Zimmerman SB, Nucleic Acids Res 1983 11 7853 7871 10.1093/nar/11.22.7853 6359064
    • (1983) Nucleic Acids Res , vol.11 , pp. 7853-7871
    • Pheiffer, B.H.1    Zimmerman, S.B.2
  • 19
    • 84863393810 scopus 로고    scopus 로고
    • Cell-specific DNA methylation patterns of retina-specific genes
    • 10.1371/journal.pone.0032602 22403679
    • Cell-specific DNA methylation patterns of retina-specific genes. Merbs SL, Khan MA, Hackler L Jr, Oliver VF, Wan J, Qian J, Zack DJ, PLoS One 2012 7 32602 10.1371/journal.pone.0032602 22403679
    • (2012) PLoS One , vol.7 , pp. 532602
    • Merbs, S.L.1    Khan, M.A.2    Hackler Jr., L.3    Oliver, V.F.4    Wan, J.5    Qian, J.6    Zack, D.J.7
  • 20
    • 0027203606 scopus 로고
    • Epigenetic mechanisms underlying the imprinting of the mouse H19 gene
    • 10.1101/gad.7.9.1663 7690336
    • Epigenetic mechanisms underlying the imprinting of the mouse H19 gene. Bartolomei MS, Webber AL, Brunkow ME, Tilghman SM, Genes Dev 1993 7 1663 1673 10.1101/gad.7.9.1663 7690336
    • (1993) Genes Dev , vol.7 , pp. 1663-1673
    • Bartolomei, M.S.1    Webber, A.L.2    Brunkow, M.E.3    Tilghman, S.M.4
  • 21
    • 0035885865 scopus 로고    scopus 로고
    • RGSZ1 and Ret RGS: Two of several splice variants from the gene RGS20
    • 10.1006/geno.2001.6659 11735229
    • RGSZ1 and Ret RGS: two of several splice variants from the gene RGS20. Barker SA, Wang J, Sierra DA, Ross EM, Genomics 2001 78 223 229 10.1006/geno.2001.6659 11735229
    • (2001) Genomics , vol.78 , pp. 223-229
    • Barker, S.A.1    Wang, J.2    Sierra, D.A.3    Ross, E.M.4
  • 24
    • 33751055189 scopus 로고    scopus 로고
    • Characterization and function of the bHLH-O protein XHes2: Insight into the mechanisms controlling retinal cell fate decision
    • 10.1242/dev.02567
    • Characterization and function of the bHLH-O protein XHes2: insight into the mechanisms controlling retinal cell fate decision. Solter M, Locker M, Boy S, Taelman V, Bellefroid EJ, Perron M, Pieler T, Development 2006 133 4097 4108 10.1242/dev.02567
    • (2006) Development , vol.133 , pp. 4097-4108
    • Solter, M.1    Locker, M.2    Boy, S.3    Taelman, V.4    Bellefroid, E.J.5    Perron, M.6    Pieler, T.7
  • 25
    • 80053172782 scopus 로고    scopus 로고
    • The long noncoding RNA Six3OS acts in trans to regulate retinal development by modulating Six3 activity
    • 10.1186/1749-8104-6-32
    • The long noncoding RNA Six3OS acts in trans to regulate retinal development by modulating Six3 activity. Rapicavoli NA, Poth EM, Zhu H, Blackshaw S, Neural Dev 2011 6 32 10.1186/1749-8104-6-32
    • (2011) Neural Dev , vol.6 , pp. 32
    • Rapicavoli, N.A.1    Poth, E.M.2    Zhu, H.3    Blackshaw, S.4
  • 26
    • 0345863999 scopus 로고    scopus 로고
    • The cholecystokinin system in the rat retina: Receptor expression and in vivo activation of tyrosine phosphorylation pathways
    • 10.1016/j.npep.2003.10.004
    • The cholecystokinin system in the rat retina: receptor expression and in vivo activation of tyrosine phosphorylation pathways. Bragado MJ, Perez-Marquez J, Garcia-Marin LJ, Neuropeptides 2003 37 374 380 10.1016/j.npep.2003.10.004
    • (2003) Neuropeptides , vol.37 , pp. 374-380
    • Bragado, M.J.1    Perez-Marquez, J.2    Garcia-Marin, L.J.3
  • 28
    • 79955777417 scopus 로고    scopus 로고
    • Genome-wide survey reveals dynamic widespread tissue-specific changes in DNA methylation during development
    • 10.1186/1471-2164-12-231 21569359
    • Genome-wide survey reveals dynamic widespread tissue-specific changes in DNA methylation during development. Liang P, Song F, Ghosh S, Morien E, Qin M, Mahmood S, Fujiwara K, Igarashi J, Nagase H, Held WA, BMC Genomics 2011 12 231 10.1186/1471-2164-12-231 21569359
    • (2011) BMC Genomics , vol.12 , pp. 231
    • Liang, P.1    Song, F.2    Ghosh, S.3    Morien, E.4    Qin, M.5    Mahmood, S.6    Fujiwara, K.7    Igarashi, J.8    Nagase, H.9    Held, W.A.10
  • 29
    • 84862210732 scopus 로고    scopus 로고
    • Functional annotation of the human brain methylome identifies tissue-specific epigenetic variation across brain and blood
    • 10.1186/gb-2012-13-6-r43 22703893
    • Functional annotation of the human brain methylome identifies tissue-specific epigenetic variation across brain and blood. Davies MN, Volta M, Pidsley R, Lunnon K, Dixit A, Lovestone S, Coarfa C, Harris RA, Milosavljevic A, Troakes C, et al. Genome Biol 2012 13 43 10.1186/gb-2012-13-6-r43 22703893
    • (2012) Genome Biol , vol.13 , pp. 1843
    • Davies, M.N.1    Volta, M.2    Pidsley, R.3    Lunnon, K.4    Dixit, A.5    Lovestone, S.6    Coarfa, C.7    Harris, R.A.8    Milosavljevic, A.9    Troakes, C.10
  • 31
  • 32
    • 53549104134 scopus 로고    scopus 로고
    • MEDME: An experimental and analytical methodology for the estimation of DNA methylation levels based on microarray derived MeDIP-enrichment
    • 10.1101/gr.080721.108 18765822
    • MEDME: an experimental and analytical methodology for the estimation of DNA methylation levels based on microarray derived MeDIP-enrichment. Pelizzola M, Koga Y, Urban AE, Krauthammer M, Weissman S, Halaban R, Molinaro AM, Genome Res 2008 18 1652 1659 10.1101/gr.080721.108 18765822
    • (2008) Genome Res , vol.18 , pp. 1652-1659
    • Pelizzola, M.1    Koga, Y.2    Urban, A.E.3    Krauthammer, M.4    Weissman, S.5    Halaban, R.6    Molinaro, A.M.7


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.