메뉴 건너뛰기




Volumn 8, Issue 9, 2013, Pages 979-989

Mapping the zebrafish brain methylome using reduced representation bisulfite sequencing

Author keywords

Brain; CpG site; DNA methylation; MspI; RRBS; Zebrafish

Indexed keywords

BISULFITE; DINUCLEOTIDE;

EID: 84883524651     PISSN: 15592294     EISSN: 15592308     Source Type: Journal    
DOI: 10.4161/epi.25797     Document Type: Article
Times cited : (59)

References (65)
  • 1
    • 47649091157 scopus 로고    scopus 로고
    • DNA methylation and structural and functional bimodality of vertebrate promoters
    • PMID:18469331
    • Elango N, Yi SV. DNA methylation and structural and functional bimodality of vertebrate promoters. Mol Biol Evol 2008; 25:1602-8; PMID:18469331; http:// dx.doi.org/10.1093/molbev/msn110
    • (2008) Mol Biol Evol , vol.25 , pp. 1602-1608
    • Elango, N.1    Yi, S.V.2
  • 2
    • 84865369147 scopus 로고    scopus 로고
    • DNA methylation dynamics during in vivo differentiation of blood and skin stem cells
    • PMID:22841485
    • Bock C, Beerman I, Lien WH, Smith ZD, Gu H, Boyle P, et al. DNA methylation dynamics during in vivo differentiation of blood and skin stem cells. Mol Cell 2012; 47:633-47; PMID:22841485; http:// dx.doi.org/10.1016/j.molcel.2012.06.019
    • (2012) Mol Cell , vol.47 , pp. 633-647
    • Bock, C.1    Beerman, I.2    Lien, W.H.3    Smith, Z.D.4    Gu, H.5    Boyle, P.6
  • 3
    • 0032833751 scopus 로고    scopus 로고
    • Absence of genomewide changes in DNA methylation during development of the zebrafish
    • PMID:10508504
    • Macleod D, Clark VH, Bird A. Absence of genomewide changes in DNA methylation during development of the zebrafish. Nat Genet 1999; 23:139-40; PMID:10508504; http://dx.doi.org/10.1038/13767
    • (1999) Nat Genet , vol.23 , pp. 139-140
    • McLeod, D.1    Clark, V.H.2    Bird, A.3
  • 4
    • 15244353967 scopus 로고    scopus 로고
    • X-inactivation profile reveals extensive variability in X-linked gene expression in females
    • PMID:15772666
    • Carrel L, Willard HF. X-inactivation profile reveals extensive variability in X-linked gene expression in females. Nature 2005; 434:400-4; PMID:15772666; http://dx.doi.org/10.1038/nature03479
    • (2005) Nature , vol.434 , pp. 400-404
    • Carrel, L.1    Willard, H.F.2
  • 5
    • 32044455298 scopus 로고    scopus 로고
    • Large-scale structure of genomic methylation patterns
    • PMID:16365381
    • Rollins RA, Haghighi F, Edwards JR, Das R, Zhang MQ, Ju J, et al. Large-scale structure of genomic methylation patterns. Genome Res 2006; 16:157-63; PMID:16365381; http://dx.doi.org/10.1101/ gr.4362006
    • (2006) Genome Res , vol.16 , pp. 157-163
    • Rollins, R.A.1    Haghighi, F.2    Edwards, J.R.3    Das, R.4    Zhang, M.Q.5    Ju, J.6
  • 6
    • 43749098985 scopus 로고    scopus 로고
    • DNA methylation landscapes: Provocative insights from epigenomics
    • PMID:18463664
    • Suzuki MM, Bird A. DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet 2008; 9:465-76; PMID:18463664; http://dx.doi. org/10.1038/nrg2341
    • (2008) Nat Rev Genet , vol.9 , pp. 465-476
    • Suzuki, M.M.1    Bird, A.2
  • 7
    • 53449100282 scopus 로고    scopus 로고
    • Quantitative analysis of human tissue-specific differences in methylation
    • PMID:18805397
    • Igarashi J, Muroi S, Kawashima H, Wang X, Shinojima Y, Kitamura E, et al. Quantitative analysis of human tissue-specific differences in methylation. Biochem Biophys Res Commun 2008; 376:658-64; PMID:18805397; http://dx.doi.org/10.1016/j. bbrc.2008.09.044
    • (2008) Biochem Biophys Res Commun , vol.376 , pp. 658-664
    • Igarashi, J.1    Muroi, S.2    Kawashima, H.3    Wang, X.4    Shinojima, Y.5    Kitamura, E.6
  • 8
    • 84868520898 scopus 로고    scopus 로고
    • Monozygotic twins: Genes are not the destiny?
    • PMID:22355239
    • Chatterjee A, Morison IM. Monozygotic twins: genes are not the destiny? Bioinformation 2011; 7:369-70; PMID:22355239; http://dx.doi. org/10.6026/97320630007369
    • (2011) Bioinformation , vol.7 , pp. 369-370
    • Chatterjee, A.1    Morison, I.M.2
  • 9
    • 0036561649 scopus 로고    scopus 로고
    • Altered methylation patterns in cancer cell genomes: Cause or consequence?
    • PMID:12086841
    • Baylin S, Bestor TH. Altered methylation patterns in cancer cell genomes: cause or consequence? Cancer Cell 2002; 1:299-305; PMID:12086841; http://dx.doi. org/10.1016/S1535-6108(02)00061-2
    • (2002) Cancer Cell , vol.1 , pp. 299-305
    • Baylin, S.1    Bestor, T.H.2
  • 10
    • 78650800283 scopus 로고    scopus 로고
    • Comprehensive profiling of zebrafish hepatic proximal promoter CpG island methylation and its modification during chemical carcinogenesis
    • PMID:21205313
    • Mirbahai L, Williams TD, Zhan H, Gong Z, Chipman JK. Comprehensive profiling of zebrafish hepatic proximal promoter CpG island methylation and its modification during chemical carcinogenesis. BMC Genomics 2011; 12:3; PMID:21205313; http:// dx.doi.org/10.1186/1471-2164-12-3
    • (2011) BMC Genomics , vol.12 , pp. 3
    • Mirbahai, L.1    Williams, T.D.2    Zhan, H.3    Gong, Z.4    Chipman, J.K.5
  • 11
    • 0029916455 scopus 로고    scopus 로고
    • Fish models for environmental carcinogenesis: The rainbow trout
    • PMID:8722107
    • Bailey GS, Williams DE, Hendricks JD. Fish models for environmental carcinogenesis: the rainbow trout. Environ Health Perspect 1996; 104(Suppl 1):5-21; PMID:8722107
    • (1996) Environ Health Perspect , vol.104 , Issue.SUPPL. 1 , pp. 5-21
    • Bailey, G.S.1    Williams, D.E.2    Hendricks, J.D.3
  • 12
    • 33749117367 scopus 로고    scopus 로고
    • Zebrafish promoter microarrays identify actively transcribed embryonic genes
    • PMID:16889661
    • Wardle FC, Odom DT, Bell GW, Yuan B, Danford TW, Wiellette EL, et al. Zebrafish promoter microarrays identify actively transcribed embryonic genes. Genome Biol 2006; 7:R71; PMID:16889661; http:// dx.doi.org/10.1186/gb-2006-7-8-r71
    • (2006) Genome Biol , vol.7
    • Wardle, F.C.1    Odom, D.T.2    Bell, G.W.3    Yuan, B.4    Danford, T.W.5    Wiellette, E.L.6
  • 13
    • 25644445324 scopus 로고    scopus 로고
    • Making waves in cancer research: New models in the zebrafish
    • PMID:16116796
    • Berghmans S, Jette C, Langenau D, Hsu K, Stewart R, Look T, et al. Making waves in cancer research: new models in the zebrafish. Biotechniques 2005; 39:227-37; PMID:16116796; http://dx.doi. org/10.2144/05392RV02
    • (2005) Biotechniques , vol.39 , pp. 227-237
    • Berghmans, S.1    Jette, C.2    Langenau, D.3    Hsu, K.4    Stewart, R.5    Look, T.6
  • 14
    • 0033052683 scopus 로고    scopus 로고
    • Zebrafish: A new model for human disease
    • PMID:10022974
    • Zon LI. Zebrafish: a new model for human disease. Genome Res 1999; 9:99-100; PMID:10022974
    • (1999) Genome Res , vol.9 , pp. 99-100
    • Zon, L.I.1
  • 15
    • 33645305405 scopus 로고    scopus 로고
    • Modeling liver cancer using zebrafish: A comparative oncogenomics approach
    • PMID:16582610
    • Lam SH, Gong Z. Modeling liver cancer using zebrafish: a comparative oncogenomics approach. Cell Cycle 2006; 5:573-7; PMID:16582610; http://dx.doi. org/10.4161/cc.5.6.2550
    • (2006) Cell Cycle , vol.5 , pp. 573-577
    • Lam, S.H.1    Gong, Z.2
  • 16
    • 30544433311 scopus 로고    scopus 로고
    • Conservation of gene expression signatures between zebrafish and human liver tumors and tumor progression
    • PMID:16327811
    • Lam SH, Wu YL, Vega VB, Miller LD, Spitsbergen J, Tong Y, et al. Conservation of gene expression signatures between zebrafish and human liver tumors and tumor progression. Nat Biotechnol 2006; 24:73-5; PMID:16327811; http://dx.doi.org/10.1038/nbt1169
    • (2006) Nat Biotechnol , vol.24 , pp. 73-75
    • Lam, S.H.1    Wu, Y.L.2    Vega, V.B.3    Miller, L.D.4    Spitsbergen, J.5    Tong, Y.6
  • 17
    • 34247186766 scopus 로고    scopus 로고
    • Animal models of human disease: Zebrafish swim into view
    • PMID:17440532
    • Lieschke GJ, Currie PD. Animal models of human disease: zebrafish swim into view. Nat Rev Genet 2007; 8:353-67; PMID:17440532; http://dx.doi. org/10.1038/nrg2091
    • (2007) Nat Rev Genet , vol.8 , pp. 353-367
    • Lieschke, G.J.1    Currie, P.D.2
  • 18
    • 80052799148 scopus 로고    scopus 로고
    • DNA methylation profiling in zebrafish
    • PMID:21924171
    • Wu SF, Zhang H, Hammoud SS, Potok M, Nix DA, Jones DA, et al. DNA methylation profiling in zebrafish. Methods Cell Biol 2011; 104:327-39; PMID:21924171; http://dx.doi.org/10.1016/B978-0-12-374814-0.00018-5
    • (2011) Methods Cell Biol , vol.104 , pp. 327-339
    • Wu, S.F.1    Zhang, H.2    Hammoud, S.S.3    Potok, M.4    Nix, D.A.5    Jones, D.A.6
  • 19
    • 79955071527 scopus 로고    scopus 로고
    • DNA methylation in zebrafish
    • PMID:21507352
    • Goll MG, Halpern ME. DNA methylation in zebrafish. Prog Mol Biol Transl Sci 2011; 101:193-218; PMID:21507352; http://dx.doi.org/10.1016/B978-0-12-387685-0.00005-6
    • (2011) Prog Mol Biol Transl Sci , vol.101 , pp. 193-218
    • Goll, M.G.1    Halpern, M.E.2
  • 20
    • 84877696605 scopus 로고    scopus 로고
    • Sperm, but not oocyte, DNA methylome is inherited by zebrafish early embryos
    • PMID:23663777
    • Jiang L, Zhang J, Wang JJ, Wang L, Zhang L, Li G, et al. Sperm, but not oocyte, DNA methylome is inherited by zebrafish early embryos. Cell 2013; 153:773-84; PMID:23663777; http://dx.doi.org/10.1016/j. cell.2013.04.041
    • (2013) Cell , vol.153 , pp. 773-784
    • Jiang, L.1    Zhang, J.2    Wang, J.J.3    Wang, L.4    Zhang, L.5    Li, G.6
  • 21
    • 84877711740 scopus 로고    scopus 로고
    • Reprogramming the maternal zebrafish genome after fertilization to match the paternal methylation pattern
    • PMID:23663776
    • Potok ME, Nix DA, Parnell TJ, Cairns BR. Reprogramming the maternal zebrafish genome after fertilization to match the paternal methylation pattern. Cell 2013; 153:759-72; PMID:23663776; http:// dx.doi.org/10.1016/j.cell.2013.04.030
    • (2013) Cell , vol.153 , pp. 759-772
    • Potok, M.E.1    Nix, D.A.2    Parnell, T.J.3    Cairns, B.R.4
  • 22
    • 4544291383 scopus 로고    scopus 로고
    • Global changes in genomic methylation levels during early development of the zebrafish embryo
    • PMID:15309635
    • Mhanni AA, McGowan RA. Global changes in genomic methylation levels during early development of the zebrafish embryo. Dev Genes Evol 2004; 214:412-7; PMID:15309635; http://dx.doi.org/10.1007/s00427-004-0418-0
    • (2004) Dev Genes Evol , vol.214 , pp. 412-417
    • Mhanni, A.A.1    McGowan, R.A.2
  • 23
    • 77952734605 scopus 로고    scopus 로고
    • Conservation and divergence of methylation patterning in plants and animals
    • PMID:20395551
    • Feng S, Cokus SJ, Zhang X, Chen PY, Bostick M, Goll MG, et al. Conservation and divergence of methylation patterning in plants and animals. Proc Natl Acad Sci U S A 2010; 107:8689-94; PMID:20395551; http:// dx.doi.org/10.1073/pnas.1002720107
    • (2010) Proc Natl Acad Sci U S A , vol.107 , pp. 8689-8694
    • Feng, S.1    Cokus, S.J.2    Zhang, X.3    Chen, P.Y.4    Bostick, M.5    Goll, M.G.6
  • 24
    • 84864936117 scopus 로고    scopus 로고
    • Developmental features of DNA methylation during activation of the embryonic zebrafish genome
    • PMID:22830626
    • Andersen IS, Reiner AH, Aanes H, Aleström P, Collas P. Developmental features of DNA methylation during activation of the embryonic zebrafish genome. Genome Biol 2012; 13:R65; PMID:22830626; http://dx.doi. org/10.1186/gb-2012-13-7-r65
    • (2012) Genome Biol , vol.13
    • Andersen, I.S.1    Reiner, A.H.2    Aanes, H.3    Aleström, P.4    Collas, P.5
  • 25
    • 77249137168 scopus 로고    scopus 로고
    • Principles and challenges of genomewide DNA methylation analysis
    • PMID:20125086
    • Laird PW. Principles and challenges of genomewide DNA methylation analysis. Nat Rev Genet 2010; 11:191-203; PMID:20125086; http://dx.doi. org/10.1038/nrg2732
    • (2010) Nat Rev Genet , vol.11 , pp. 191-203
    • Laird, P.W.1
  • 26
    • 49649125042 scopus 로고    scopus 로고
    • Genome-scale DNA methylation maps of pluripotent and differentiated cells
    • PMID:18600261
    • Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, Sivachenko A, et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 2008; 454:766-70; PMID:18600261
    • (2008) Nature , vol.454 , pp. 766-770
    • Meissner, A.1    Mikkelsen, T.S.2    Gu, H.3    Wernig, M.4    Hanna, J.5    Sivachenko, A.6
  • 27
    • 80052306947 scopus 로고    scopus 로고
    • Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation
    • PMID:21852959
    • Gertz J, Varley KE, Reddy TE, Bowling KM, Pauli F, Parker SL, et al. Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation. PLoS Genet 2011; 7:e1002228; PMID:21852959; http://dx.doi. org/10.1371/journal.pgen.1002228
    • (2011) PLoS Genet , vol.7
    • Gertz, J.1    Varley, K.E.2    Reddy, T.E.3    Bowling, K.M.4    Pauli, F.5    Parker, S.L.6
  • 28
    • 79551677421 scopus 로고    scopus 로고
    • Reference Maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines
    • PMID:21295703
    • Bock C, Kiskinis E, Verstappen G, Gu H, Boulting G, Smith ZD, et al. Reference Maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines. Cell 2011; 144:439-52; PMID:21295703; http://dx.doi.org/10.1016/j. cell.2010.12.032
    • (2011) Cell , vol.144 , pp. 439-452
    • Bock, C.1    Kiskinis, E.2    Verstappen, G.3    Gu, H.4    Boulting, G.5    Smith, Z.D.6
  • 29
    • 79955510962 scopus 로고    scopus 로고
    • Genes methylated by DNA methyltransferase 3b are similar in mouse intestine and human colon cancer
    • PMID:21490393
    • Steine EJ, Ehrich M, Bell GW, Raj A, Reddy S, van Oudenaarden A, et al. Genes methylated by DNA methyltransferase 3b are similar in mouse intestine and human colon cancer. J Clin Invest 2011; 121:1748-52; PMID:21490393; http://dx.doi.org/10.1172/ JCI43169
    • (2011) J Clin Invest , vol.121 , pp. 1748-1752
    • Steine, E.J.1    Ehrich, M.2    Bell, G.W.3    Raj, A.4    Reddy, S.5    van Oudenaarden, A.6
  • 30
    • 79955557706 scopus 로고    scopus 로고
    • Neurons show distinctive DNA methylation profile and higher interindividual variations compared with non-neurons
    • PMID:21467265
    • Iwamoto K, Bundo M, Ueda J, Oldham MC, Ukai W, Hashimoto E, et al. Neurons show distinctive DNA methylation profile and higher interindividual variations compared with non-neurons. Genome Res 2011; 21:688-96; PMID:21467265; http://dx.doi. org/10.1101/gr.112755.110
    • (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
  • 31
    • 54849426071 scopus 로고    scopus 로고
    • Epigenetic regulation of BDNF gene transcription in the consolidation of fear memory
    • PMID:18923034
    • Lubin FD, Roth TL, Sweatt JD. Epigenetic regulation of BDNF gene transcription in the consolidation of fear memory. J Neurosci 2008; 28:10576-86; PMID:18923034; http://dx.doi.org/10.1523/ JNEUROSCI.1786-08.2008
    • (2008) J Neurosci , vol.28 , pp. 10576-10586
    • Lubin, F.D.1    Roth, T.L.2    Sweatt, J.D.3
  • 32
    • 77958605856 scopus 로고    scopus 로고
    • Epigenetic choreographers of neurogenesis in the adult mammalian brain
    • PMID:20975758
    • Ma DK, Marchetto MC, Guo JU, Ming GL, Gage FH, Song H. Epigenetic choreographers of neurogenesis in the adult mammalian brain. Nat Neurosci 2010; 13:1338-44; PMID:20975758; http://dx.doi. org/10.1038/nn.2672
    • (2010) Nat Neurosci , vol.13 , pp. 1338-1344
    • Ma, D.K.1    Marchetto, M.C.2    Guo, J.U.3    Ming, G.L.4    Gage, F.H.5    Song, H.6
  • 33
    • 67649185049 scopus 로고    scopus 로고
    • Genetics, environmental factors and the emerging role of epigenetics in neurodegenerative diseases
    • PMID:19026668
    • Migliore L, Coppedè F. Genetics, environmental factors and the emerging role of epigenetics in neurodegenerative diseases. Mutat Res 2009; 667:82-97; PMID:19026668; http://dx.doi.org/10.1016/j.mrfmmm. 2008.10.011
    • (2009) Mutat Res , vol.667 , pp. 82-97
    • Migliore, L.1    Coppedè, F.2
  • 34
    • 79958025812 scopus 로고    scopus 로고
    • Complexities of Rett syndrome and MeCP2
    • PMID:21632916
    • Samaco RC, Neul JL. Complexities of Rett syndrome and MeCP2. J Neurosci 2011; 31:7951-9; PMID:21632916; http://dx.doi.org/10.1523/ JNEUROSCI.0169-11.2011
    • (2011) J Neurosci , vol.31 , pp. 7951-7959
    • Samaco, R.C.1    Neul, J.L.2
  • 35
    • 41149140859 scopus 로고    scopus 로고
    • Epigenomic profiling reveals DNA-methylation changes associated with major psychosis
    • PMID:18319075
    • Mill J, Tang T, Kaminsky Z, Khare T, Yazdanpanah S, Bouchard L, et al. Epigenomic profiling reveals DNA-methylation changes associated with major psychosis. Am J Hum Genet 2008; 82:696-711; PMID:18319075; http://dx.doi.org/10.1016/j. ajhg.2008.01.008
    • (2008) Am J Hum Genet , vol.82 , pp. 696-711
    • Mill, J.1    Tang, T.2    Kaminsky, Z.3    Khare, T.4    Yazdanpanah, S.5    Bouchard, L.6
  • 36
    • 84871398317 scopus 로고    scopus 로고
    • CTCF/cohesin-mediated DNA looping is required for protocadherin α promoter choice
    • PMID:23204437
    • Guo Y, Monahan K, Wu H, Gertz J, Varley KE, Li W, et al. CTCF/cohesin-mediated DNA looping is required for protocadherin α promoter choice. Proc Natl Acad Sci U S A 2012; 109:21081-6; PMID:23204437; http://dx.doi.org/10.1073/pnas.1219280110
    • (2012) Proc Natl Acad Sci U S A , vol.109 , pp. 21081-21086
    • Guo, Y.1    Monahan, K.2    Wu, H.3    Gertz, J.4    Varley, K.E.5    Li, W.6
  • 37
    • 84861563688 scopus 로고    scopus 로고
    • Comparison of alignment software for genome-wide bisulphite sequence data
    • PMID:22344695
    • Chatterjee A, Stockwell PA, Rodger EJ, Morison IM. Comparison of alignment software for genome-wide bisulphite sequence data. Nucleic Acids Res 2012; 40:e79; PMID:22344695; http://dx.doi.org/10.1093/ nar/gks150
    • (2012) Nucleic Acids Res , vol.40
    • Chatterjee, A.1    Stockwell, P.A.2    Rodger, E.J.3    Morison, I.M.4
  • 38
    • 84860577302 scopus 로고    scopus 로고
    • Diametrically opposite methylome-transcriptome relationships in high-and low-CpG promoter genes in postmitotic neural rat tissue
    • PMID:22415013
    • Hartung T, Zhang L, Kanwar R, Khrebtukova I, Reinhardt M, Wang C, et al. Diametrically opposite methylome-transcriptome relationships in high-and low-CpG promoter genes in postmitotic neural rat tissue. Epigenetics 2012; 7:421-8; PMID:22415013; http://dx.doi.org/10.4161/epi.19565
    • (2012) Epigenetics , vol.7 , pp. 421-428
    • Hartung, T.1    Zhang, L.2    Kanwar, R.3    Khrebtukova, I.4    Reinhardt, M.5    Wang, C.6
  • 39
    • 22244454037 scopus 로고    scopus 로고
    • Identification of a gene required for de novo DNA methylation of the zebrafish no tail gene
    • PMID:15937923
    • Shimoda N, Yamakoshi K, Miyake A, Takeda H. Identification of a gene required for de novo DNA methylation of the zebrafish no tail gene. Dev Dyn 2005; 233:1509-16; PMID:15937923; http://dx.doi. org/10.1002/dvdy.20455
    • (2005) Dev Dyn , vol.233 , pp. 1509-1516
    • Shimoda, N.1    Yamakoshi, K.2    Miyake, A.3    Takeda, H.4
  • 40
    • 70249128067 scopus 로고    scopus 로고
    • Transcriptional silencing and reactivation in transgenic zebrafish
    • PMID:19433629
    • Goll MG, Anderson R, Stainier DY, Spradling AC, Halpern ME. Transcriptional silencing and reactivation in transgenic zebrafish. Genetics 2009; 182:747-55; PMID:19433629; http://dx.doi.org/10.1534/genetics. 109.102079
    • (2009) Genetics , vol.182 , pp. 747-755
    • Goll, M.G.1    Anderson, R.2    Stainier, D.Y.3    Spradling, A.C.4    Halpern, M.E.5
  • 41
    • 57649196594 scopus 로고    scopus 로고
    • DNA demethylation in zebrafish involves the coupling of a deaminase, a glycosylase, and gadd45
    • PMID:19109892
    • Rai K, Huggins IJ, James SR, Karpf AR, Jones DA, Cairns BR. DNA demethylation in zebrafish involves the coupling of a deaminase, a glycosylase, and gadd45. Cell 2008; 135:1201-12; PMID:19109892; http:// dx.doi.org/10.1016/j.cell.2008.11.042
    • (2008) Cell , vol.135 , pp. 1201-1212
    • Rai, K.1    Huggins, I.J.2    James, S.R.3    Karpf, A.R.4    Jones, D.A.5    Cairns, B.R.6
  • 42
    • 84857331867 scopus 로고    scopus 로고
    • Base-resolution analyses of sequence and parentof-origin dependent DNA methylation in the mouse genome
    • PMID:22341451
    • Xie W, Barr CL, Kim A, Yue F, Lee AY, Eubanks J, et al. Base-resolution analyses of sequence and parentof-origin dependent DNA methylation in the mouse genome. Cell 2012; 148:816-31; PMID:22341451; http://dx.doi.org/10.1016/j.cell.2011.12.035
    • (2012) Cell , vol.148 , pp. 816-831
    • Xie, W.1    Barr, C.L.2    Kim, A.3    Yue, F.4    Lee, A.Y.5    Eubanks, J.6
  • 43
    • 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
    • PMID:23324053
    • Wang J, Xia Y, Li L, Gong D, Yao Y, Luo H, et al. Double restriction-enzyme digestion improves the coverage and accuracy of genome-wide CpG methylation profiling by reduced representation bisulfite sequencing. BMC Genomics 2013; 14:11; PMID:23324053; http://dx.doi.org/10.1186/1471-2164-14-11
    • (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
  • 44
    • 84876807823 scopus 로고    scopus 로고
    • A systematic genome-wide analysis of zebrafish protein-coding gene function
    • PMID:23594742
    • Kettleborough RN, Busch-Nentwich EM, Harvey SA, Dooley CM, de Bruijn E, van Eeden F, et al. A systematic genome-wide analysis of zebrafish protein-coding gene function. Nature 2013; 496:494-7; PMID:23594742; http://dx.doi.org/10.1038/ nature11992
    • (2013) Nature , vol.496 , pp. 494-497
    • Kettleborough, R.N.1    Busch-Nentwich, E.M.2    Harvey, S.A.3    Dooley, C.M.4    de Bruijn, E.5    van Eeden, F.6
  • 45
    • 84876798186 scopus 로고    scopus 로고
    • The zebrafish reference genome sequence and its relationship to the human genome
    • PMID:23594743
    • Howe K, Clark MD, Torroja CF, Torrance J, Berthelot C, Muffato M, et al. The zebrafish reference genome sequence and its relationship to the human genome. Nature 2013; 496:498-503; PMID:23594743; http:// dx.doi.org/10.1038/nature12111
    • (2013) Nature , vol.496 , pp. 498-503
    • Howe, K.1    Clark, M.D.2    Torroja, C.F.3    Torrance, J.4    Berthelot, C.5    Muffato, M.6
  • 46
    • 31944432339 scopus 로고    scopus 로고
    • A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters
    • PMID:16432200
    • Saxonov S, Berg P, Brutlag DL. A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc Natl Acad Sci U S A 2006; 103:1412-7; PMID:16432200; http://dx.doi.org/10.1073/pnas.0510310103
    • (2006) Proc Natl Acad Sci U S A , vol.103 , pp. 1412-1417
    • Saxonov, S.1    Berg, P.2    Brutlag, D.L.3
  • 47
    • 0037133565 scopus 로고    scopus 로고
    • Comprehensive analysis of CpG islands in human chromosomes 21 and 22
    • PMID:11891299
    • Takai D, Jones PA. Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proc Natl Acad Sci U S A 2002; 99:3740-5; PMID:11891299; http://dx.doi.org/10.1073/pnas.052410099
    • (2002) Proc Natl Acad Sci U S A , vol.99 , pp. 3740-3745
    • Takai, D.1    Jones, P.A.2
  • 48
    • 0023216891 scopus 로고
    • CpG islands in vertebrate genomes
    • PMID:3656447
    • Gardiner-Garden M, Frommer M. CpG islands in vertebrate genomes. J Mol Biol 1987; 196:261-82; PMID:3656447; http://dx.doi.org/10.1016/0022-2836(87)90689-9
    • (1987) J Mol Biol , vol.196 , pp. 261-282
    • Gardiner-Garden, M.1    Frommer, M.2
  • 49
    • 59149084538 scopus 로고    scopus 로고
    • The human colon cancer methylome shows similar hypo-and hypermethylation at conserved tissue-specific CpG island shores
    • PMID:19151715
    • Irizarry RA, Ladd-Acosta C, Wen B, Wu Z, Montano C, Onyango P, et al. The human colon cancer methylome shows similar hypo-and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet 2009; 41:178-86; PMID:19151715; http://dx.doi. org/10.1038/ng.298
    • (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
  • 50
    • 70649095120 scopus 로고    scopus 로고
    • Differential methylation of tissueand cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts
    • PMID:19881528
    • Doi A, Park IH, Wen B, Murakami P, Aryee MJ, Irizarry R, et al. Differential methylation of tissueand cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts. Nat Genet 2009; 41:1350-3; PMID:19881528; http://dx.doi.org/10.1038/ng.471
    • (2009) Nat Genet , vol.41 , pp. 1350-1353
    • Doi, A.1    Park, I.H.2    Wen, B.3    Murakami, P.4    Aryee, M.J.5    Irizarry, R.6
  • 51
    • 77649267695 scopus 로고    scopus 로고
    • Dynamic changes in the human methylome during differentiation
    • PMID:20133333
    • Laurent L, Wong E, Li G, Huynh T, Tsirigos A, Ong CT, et al. Dynamic changes in the human methylome during differentiation. Genome Res 2010; 20:320-31; PMID:20133333; http://dx.doi.org/10.1101/ gr.101907.109
    • (2010) Genome Res , vol.20 , pp. 320-331
    • Laurent, L.1    Wong, E.2    Li, G.3    Huynh, T.4    Tsirigos, A.5    Ong, C.T.6
  • 52
    • 80455176999 scopus 로고    scopus 로고
    • CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing
    • PMID:21964334
    • Shukla S, Kavak E, Gregory M, Imashimizu M, Shutinoski B, Kashlev M, et al. CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing. Nature 2011; 479:74-9; PMID:21964334; http:// dx.doi.org/10.1038/nature10442
    • (2011) Nature , vol.479 , pp. 74-79
    • Shukla, S.1    Kavak, E.2    Gregory, M.3    Imashimizu, M.4    Shutinoski, B.5    Kashlev, M.6
  • 53
    • 79955400147 scopus 로고    scopus 로고
    • Relationship between gene body DNA methylation and intragenic H3K9me3 and H3K36me3 chromatin marks
    • PMID:21526191
    • Hahn MA, Wu X, Li AX, Hahn T, Pfeifer GP. Relationship between gene body DNA methylation and intragenic H3K9me3 and H3K36me3 chromatin marks. PLoS One 2011; 6:e18844; PMID:21526191; http://dx.doi.org/10.1371/journal.pone.0018844
    • (2011) PLoS One , vol.6
    • Hahn, M.A.1    Wu, X.2    Li, A.X.3    Hahn, T.4    Pfeifer, G.P.5
  • 54
    • 78751693154 scopus 로고    scopus 로고
    • Replication timing-related and gene body-specific methylation of active human genes
    • PMID:21112978
    • Aran D, Toperoff G, Rosenberg M, Hellman A. Replication timing-related and gene body-specific methylation of active human genes. Hum Mol Genet 2011; 20:670-80; PMID:21112978; http://dx.doi. org/10.1093/hmg/ddq513
    • (2011) Hum Mol Genet , vol.20 , pp. 670-680
    • Aran, D.1    Toperoff, G.2    Rosenberg, M.3    Hellman, A.4
  • 55
    • 70450217879 scopus 로고    scopus 로고
    • Human DNA methylomes at base resolution show widespread epigenomic differences
    • PMID:19829295
    • Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 2009; 462:315-22; PMID:19829295; http://dx.doi.org/10.1038/nature08514
    • (2009) Nature , vol.462 , pp. 315-322
    • Lister, R.1    Pelizzola, M.2    Dowen, R.H.3    Hawkins, R.D.4    Hon, G.5    Tonti-Filippini, J.6
  • 56
    • 0029445204 scopus 로고
    • Studies of DNA methylation in animals
    • PMID:8655645
    • Bird A, Tate P, Nan X, Campoy J, Meehan R, Cross S, et al. Studies of DNA methylation in animals. J Cell Sci Suppl 1995; 19:37-9; PMID:8655645; http://dx.doi. org/10.1242/jcs.1995.Supplement_19.5
    • (1995) J Cell Sci Suppl , vol.19 , pp. 37-39
    • Bird, A.1    Tate, P.2    Nan, X.3    Campoy, J.4    Meehan, R.5    Cross, S.6
  • 57
    • 84867145980 scopus 로고    scopus 로고
    • On the presence and role of human gene-body DNA methylation
    • PMID:22577155
    • Jjingo D, Conley AB, Yi SV, Lunyak VV, Jordan IK. On the presence and role of human gene-body DNA methylation. Oncotarget 2012; 3:462-74; PMID:22577155
    • (2012) Oncotarget , vol.3 , pp. 462-474
    • Jjingo, D.1    Conley, A.B.2    Yi, S.V.3    Lunyak, V.V.4    Jordan, I.K.5
  • 58
    • 84867158452 scopus 로고    scopus 로고
    • Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis
    • PMID:22593555
    • Bogdanovic O, Fernandez-Miñán A, Tena JJ, de la Calle-Mustienes E, Hidalgo C, van Kruysbergen I, et al. Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis. Genome Res 2012; 22:2043-53; PMID:22593555; http://dx.doi.org/10.1101/ gr.134833.111
    • (2012) Genome Res , vol.22 , pp. 2043-2053
    • Bogdanovic, O.1    Fernandez-Miñán, A.2    Tena, J.J.3    de la Calle-Mustienes, E.4    Hidalgo, C.5    van Kruysbergen, I.6
  • 59
    • 84868689387 scopus 로고    scopus 로고
    • Long distance relationships: Enhancer-promoter communication and dynamic gene transcription
    • PMID:23124110
    • Marsman J, Horsfield JA. Long distance relationships: enhancer-promoter communication and dynamic gene transcription. Biochim Biophys Acta 2012; 1819:1217-27; PMID:23124110; http://dx.doi.org/10.1016/j. bbagrm.2012.10.008
    • (2012) Biochim Biophys Acta , vol.1819 , pp. 1217-1227
    • Marsman, J.1    Horsfield, J.A.2
  • 60
    • 84867322151 scopus 로고    scopus 로고
    • 5-Hydroxymethylcytosine-the elusive epigenetic mark in mammalian DNA
    • PMID:22842880
    • Kriukiene E, Liutkeviciute Z, Klimašauskas S. 5-Hydroxymethylcytosine-the elusive epigenetic mark in mammalian DNA. Chem Soc Rev 2012; 41:6916-30; PMID:22842880; http://dx.doi.org/10.1039/ c2cs35104h
    • (2012) Chem Soc Rev , vol.41 , pp. 6916-6930
    • Kriukiene, E.1    Liutkeviciute, Z.2    Klimašauskas, S.3
  • 61
    • 84869013266 scopus 로고    scopus 로고
    • Technical considerations for reduced representation bisulfite sequencing with multiplexed libraries
    • PMID:23193365
    • Chatterjee A, Rodger EJ, Stockwell PA, Weeks RJ, Morison IM. Technical considerations for reduced representation bisulfite sequencing with multiplexed libraries. J Biomed Biotechnol 2012; 2012:741542; PMID:23193365; http://dx.doi. org/10.1155/2012/741542
    • (2012) J Biomed Biotechnol , vol.2012 , pp. 741542
    • Chatterjee, A.1    Rodger, E.J.2    Stockwell, P.A.3    Weeks, R.J.4    Morison, I.M.5
  • 62
    • 79957868920 scopus 로고    scopus 로고
    • Bismark: A flexible aligner and methylation caller for Bisulfite-Seq applications
    • PMID:21493656
    • Krueger F, Andrews SR. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 2011; 27:1571-2; PMID:21493656; http://dx.doi.org/10.1093/bioinformatics/btr167
    • (2011) Bioinformatics , vol.27 , pp. 1571-1572
    • Krueger, F.1    Andrews, S.R.2
  • 63
    • 84866860221 scopus 로고    scopus 로고
    • methylKit: A comprehensive R package for the analysis of genomewide DNA methylation profiles
    • PMID:23034086
    • Akalin A, Kormaksson M, Li S, Garrett-Bakelman FE, Figueroa ME, Melnick A, et al. methylKit: a comprehensive R package for the analysis of genomewide DNA methylation profiles. Genome Biol 2012; 13:R87; PMID:23034086; http://dx.doi.org/10.1186/ gb-2012-13-10-r87
    • (2012) Genome Biol , vol.13
    • Akalin, A.1    Kormaksson, M.2    Li, S.3    Garrett-Bakelman, F.E.4    Figueroa, M.E.5    Melnick, A.6
  • 64
    • 84858150703 scopus 로고    scopus 로고
    • MethylomeDB: A database of DNA methylation profiles of the brain
    • PMID:22140101;, Database issu
    • Xin Y, Chanrion B, O'Donnell AH, Milekic M, Costa R, Ge Y, et al. MethylomeDB: a database of DNA methylation profiles of the brain. Nucleic Acids Res 2012; 40(Database issue):D1245-9; PMID:22140101; http://dx.doi.org/10.1093/nar/gkr1193
    • (2012) Nucleic Acids Res , vol.40
    • Xin, Y.1    Chanrion, B.2    O'Donnell, A.H.3    Milekic, M.4    Costa, R.5    Ge, Y.6
  • 65
    • 67649854923 scopus 로고    scopus 로고
    • High-throughput bisulfite sequencing in mammalian genomes
    • PMID:19442738
    • Smith ZD, Gu H, Bock C, Gnirke A, Meissner A. High-throughput bisulfite sequencing in mammalian genomes. Methods 2009; 48:226-32; PMID:19442738; http://dx.doi.org/10.1016/j.ymeth.2009.05.003
    • (2009) Methods , vol.48 , pp. 226-232
    • Smith, Z.D.1    Gu, H.2    Bock, C.3    Gnirke, A.4    Meissner, A.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.