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Volumn 3, Issue , 2013, Pages

Quantitative epigenetic co-variation in CpG islands and co-regulation of developmental genes

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE; TRANSCRIPTOME;

EID: 84883764464     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep02576     Document Type: Article
Times cited : (19)

References (54)
  • 1
    • 38649108184 scopus 로고    scopus 로고
    • Unraveling Epigenetic Regulation in Embryonic Stem Cells
    • DOI 10.1016/j.stem.2008.01.005, PII S1934590908000064
    • Bibikova, M., Laurent, L. C., Ren, B., Loring, J. F.&Fan, J. B. Unraveling epigenetic regulation in embryonic stem cells. Cell Stem Cell 2, 123-134 (2008). (Pubitemid 351168715)
    • (2008) Cell Stem Cell , vol.2 , Issue.2 , pp. 123-134
    • Bibikova, M.1    Laurent, L.C.2    Ren, B.3    Loring, J.F.4    Fan, J.-B.5
  • 2
    • 0022540321 scopus 로고
    • CpG-rich islands and the function of DNA methylation
    • Bird, A. P. CpG-rich islands and the function of DNA methylation. Nature 321, 209-213 (1986). (Pubitemid 16016411)
    • (1986) Nature , vol.321 , Issue.6067 , pp. 209-213
    • Bird, A.P.1
  • 4
    • 79956330964 scopus 로고    scopus 로고
    • CpG islands and the regulation of transcription
    • Deaton, A. M. & Bird, A. CpG islands and the regulation of transcription. Genes Dev 25, 1010-1022 (2011).
    • (2011) Genes Dev , vol.25 , pp. 1010-1022
    • Deaton, A.M.1    Bird, A.2
  • 5
    • 49649125042 scopus 로고    scopus 로고
    • Genome-scale DNA methylation maps of pluripotent and differentiated cells
    • Meissner, A. et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454, 766-770 (2008).
    • (2008) Nature , vol.454 , pp. 766-770
    • Meissner, A.1
  • 6
    • 84869880642 scopus 로고    scopus 로고
    • Human genes with CpG island promoters have a distinct transcription-associated chromatin organization
    • Vavouri, T. & Lehner, B. Human genes with CpG island promoters have a distinct transcription-associated chromatin organization. Genome Biol 13, R110 (2012).
    • (2012) Genome Biol , vol.13
    • Vavouri, T.1    Lehner, B.2
  • 7
    • 77950882645 scopus 로고    scopus 로고
    • CpG islands recruit a histone H3 lysine 36 demethylase
    • Blackledge, N. P. et al.CpG islands recruit a histone H3 lysine 36 demethylase. Mol Cell 38, 179-190 (2010).
    • (2010) Mol Cell , vol.38 , pp. 179-190
    • Blackledge, N.P.1
  • 8
    • 77951116072 scopus 로고    scopus 로고
    • CpG islands influence chromatin structure via the CpGbinding protein Cfp1
    • Thomson, J. P. et al. CpG islands influence chromatin structure via the CpGbinding protein Cfp1. Nature 464, 1082-1086 (2010).
    • (2010) Nature , vol.464 , pp. 1082-1086
    • Thomson, J.P.1
  • 9
    • 78650684739 scopus 로고    scopus 로고
    • GC-rich sequence elements recruit PRC2 in mammalian ES cells
    • Mendenhall, E. M. et al. GC-rich sequence elements recruit PRC2 in mammalian ES cells. PLoS genetics 6, e1001244 (2010).
    • (2010) PLoS Genetics , vol.6
    • Mendenhall, E.M.1
  • 10
    • 67049159825 scopus 로고    scopus 로고
    • SHRiMP: Accurate mapping of short color-space reads
    • Rumble, S. M. et al. SHRiMP: accurate mapping of short color-space reads. PLoS computational biology 5, e1000386 (2009).
    • (2009) PLoS Computational Biology , vol.5
    • Rumble, S.M.1
  • 11
    • 53549128365 scopus 로고    scopus 로고
    • A mono-allelic bivalent chromatin domain controls tissuespecific imprinting at Grb10
    • Sanz, L. A. et al. A mono-allelic bivalent chromatin domain controls tissuespecific imprinting at Grb10. EMBO J 27, 2523-2532 (2008).
    • (2008) EMBO J , vol.27 , pp. 2523-2532
    • Sanz, L.A.1
  • 14
    • 79960926869 scopus 로고    scopus 로고
    • Integrative network biology: Graph prototyping for co-expression cancer networks
    • Kugler, K. G., Mueller, L. A., Graber, A. & Dehmer, M. Integrative network biology: graph prototyping for co-expression cancer networks. PLoS One 6, e22843 (2011).
    • (2011) PLoS One , vol.6
    • Kugler, K.G.1    Mueller, L.A.2    Graber, A.3    Dehmer, M.4
  • 15
    • 84861883921 scopus 로고    scopus 로고
    • Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk
    • Brinkman, A. B. et al. Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk. Genome Res 22, 1128-1138 (2012).
    • (2012) Genome Res , vol.22 , pp. 1128-1138
    • Brinkman, A.B.1
  • 16
    • 78649956430 scopus 로고    scopus 로고
    • Discovering cooperative relationships of chromatin modifications in human T cells based on a proposed closeness measure
    • Lv, J. et al. Discovering cooperative relationships of chromatin modifications in human T cells based on a proposed closeness measure. PLoS ONE 5, e14219 (2010).
    • (2010) PLoS ONE , vol.5
    • Lv, J.1
  • 17
    • 0036733675 scopus 로고    scopus 로고
    • Chromatin modification and epigenetic reprogramming in mammalian development
    • DOI 10.1038/nrg887
    • Li, E. Chromatin modification and epigenetic reprogramming in mammalian development. Nat Rev Genet 3, 662-673 (2002). (Pubitemid 34984255)
    • (2002) Nature Reviews Genetics , vol.3 , Issue.9 , pp. 662-673
    • Li, E.1
  • 18
    • 84863011941 scopus 로고    scopus 로고
    • Local chromatin dynamics of transcription factors imply cell-lineage specific functions during cellular differentiation
    • Tian, R., Feng, J., Cai, X. & Zhang, Y. Local chromatin dynamics of transcription factors imply cell-lineage specific functions during cellular differentiation. Epigenetics 7, 55-62 (2012).
    • (2012) Epigenetics , vol.7 , pp. 55-62
    • Tian, R.1    Feng, J.2    Cai, X.3    Zhang, Y.4
  • 19
    • 84856528270 scopus 로고    scopus 로고
    • Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer
    • Hon, G. C. et al. Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Res 22, 246-258 (2012).
    • (2012) Genome Res , vol.22 , pp. 246-258
    • Hon, G.C.1
  • 20
    • 79957863741 scopus 로고    scopus 로고
    • Capturing the dynamic epigenome
    • Deal, R. B. &Henikoff, S. Capturing the dynamic epigenome. Genome Biol 11, 218 (2010).
    • (2010) Genome Biol , vol.11 , pp. 218
    • Deal, R.B.1    Henikoff, S.2
  • 21
    • 53749092745 scopus 로고    scopus 로고
    • An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data
    • Xu, H., Wei, C. L., Lin, F. & Sung, W. K. An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data. Bioinformatics 24, 2344-2349 (2008).
    • (2008) Bioinformatics , vol.24 , pp. 2344-2349
    • Xu, H.1    Wei, C.L.2    Lin, F.3    Sung, W.K.4
  • 22
    • 79957869355 scopus 로고    scopus 로고
    • DIME: R-package for identifying differential ChIPseq based on an ensemble of mixture models
    • Taslim, C., Huang, T. &Lin, S. DIME: R-package for identifying differential ChIPseq based on an ensemble of mixture models. Bioinformatics 27, 1569-1570 (2011).
    • (2011) Bioinformatics , vol.27 , pp. 1569-1570
    • Taslim, C.1    Huang, T.2    Lin, S.3
  • 23
    • 79956006215 scopus 로고    scopus 로고
    • QDMR: A quantitative method for identification of differentially methylated regions by entropy
    • Zhang, Y. et al. QDMR: a quantitative method for identification of differentially methylated regions by entropy. Nucleic Acids Res 39, e58 (2011).
    • (2011) Nucleic Acids Res , vol.39
    • Zhang, Y.1
  • 24
    • 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, 315-322 (2009).
    • (2009) Nature , vol.462 , pp. 315-322
    • Lister, R.1
  • 25
    • 76749135286 scopus 로고    scopus 로고
    • Intergenic, gene terminal, and intragenic CpG islands in the human genome
    • Medvedeva, Y. A. et al. Intergenic, gene terminal, and intragenic CpG islands in the human genome. BMC genomics 11, 48 (2010).
    • (2010) BMC Genomics , vol.11 , pp. 48
    • Medvedeva, Y.A.1
  • 26
    • 79959872458 scopus 로고    scopus 로고
    • Cell type-specific DNA methylation at intragenic CpG islands in the immune system
    • Deaton, A.M. et al. Cell type-specific DNA methylation at intragenic CpG islands in the immune system. Genome Res 21, 1074-1086 (2011).
    • (2011) Genome Res , vol.21 , pp. 1074-1086
    • Deaton, A.M.1
  • 27
    • 84874816208 scopus 로고    scopus 로고
    • DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes
    • Aran, D., Sabato, S. & Hellman, A. DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes. Genome Biology 14 (2013).
    • (2013) Genome Biology , vol.14
    • Aran, D.1    Sabato, S.2    Hellman, A.3
  • 30
    • 69649109364 scopus 로고    scopus 로고
    • Circos: An information aesthetic for comparative genomics
    • Krzywinski, M. et al. Circos: an information aesthetic for comparative genomics. Genome Res 19, 1639-1645 (2009).
    • (2009) Genome Res , vol.19 , pp. 1639-1645
    • Krzywinski, M.1
  • 31
    • 82855176833 scopus 로고    scopus 로고
    • Epigenetic reprogramming in mouse preimplantation development and primordial germ cells
    • Saitou, M.,Kagiwada, S.&Kurimoto, K. Epigenetic reprogramming in mouse preimplantation development and primordial germ cells. Development 139, 15-31 (2012).
    • (2012) Development , vol.139 , pp. 15-31
    • Saitou, M.1    Kagiwada, S.2    Kurimoto, K.3
  • 32
    • 60849089645 scopus 로고    scopus 로고
    • Aberrant DNA methylation is a dominant mechanism in MDS progression to AML
    • Jiang, Y. et al. Aberrant DNA methylation is a dominant mechanism in MDS progression to AML. Blood 113, 1315-1325 (2009).
    • (2009) Blood , vol.113 , pp. 1315-1325
    • Jiang, Y.1
  • 34
    • 1242316153 scopus 로고    scopus 로고
    • A Postmitotic Role for Isl-Class LIM Homeodomain Proteins in the Assignment of Visceral Spinal Motor Neuron Identity
    • DOI 10.1016/S0896-6273(04)00011-X
    • Thaler, J. P. et al. A postmitotic role for Isl-class LIM homeodomain proteins in the assignment of visceral spinal motor neuron identity. Neuron 41, 337-350 (2004). (Pubitemid 38221039)
    • (2004) Neuron , vol.41 , Issue.3 , pp. 337-350
    • Thaler, J.P.1    Koo, S.J.2    Kania, A.3    Lettieri, K.4    Andrews, S.5    Cox, C.6    Jessell, T.M.7    Pfaff, S.L.8
  • 36
    • 64549090667 scopus 로고    scopus 로고
    • CDKN1C (p57) is a direct target of EZH2 and suppressed by multiple epigenetic mechanisms in breast cancer cells
    • Yang, X. et al. CDKN1C (p57) is a direct target of EZH2 and suppressed by multiple epigenetic mechanisms in breast cancer cells. PLoS One 4, e5011 (2009).
    • (2009) PLoS One , vol.4
    • Yang, X.1
  • 37
    • 0025975985 scopus 로고
    • DNA methylation inhibits transcription indirectly via a methyl-CpG binding protein
    • Boyes, J. & Bird, A. DNA methylation inhibits transcription indirectly via a methyl-CpG binding protein. Cell 64, 1123-1134 (1991). (Pubitemid 121001199)
    • (1991) Cell , vol.64 , Issue.6 , pp. 1123-1134
    • Boyes, J.1    Bird, A.2
  • 40
    • 67349190247 scopus 로고    scopus 로고
    • Linking DNA methylation and histone modification: Patterns and paradigms
    • Cedar, H. & Bergman, Y. Linking DNA methylation and histone modification: patterns and paradigms. Nat Rev Genet 10, 295-304 (2009).
    • (2009) Nat Rev Genet , vol.10 , pp. 295-304
    • Cedar, H.1    Bergman, Y.2
  • 41
    • 33747195353 scopus 로고    scopus 로고
    • Induction of Pluripotent Stem Cells from Mouse Embryonic and Adult Fibroblast Cultures by Defined Factors
    • DOI 10.1016/j.cell.2006.07.024, PII S0092867406009767
    • Takahashi, K. & Yamanaka, S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126, 663-676 (2006). (Pubitemid 44233629)
    • (2006) Cell , vol.126 , Issue.4 , pp. 663-676
    • Takahashi, K.1    Yamanaka, S.2
  • 42
    • 77649267695 scopus 로고    scopus 로고
    • Dynamic changes in the human methylome during differentiation
    • Laurent, L. et al. Dynamic changes in the human methylome during differentiation. Genome Res 20, 320-331 (2010).
    • (2010) Genome Res , vol.20 , pp. 320-331
    • Laurent, L.1
  • 43
    • 37549008674 scopus 로고    scopus 로고
    • C-Myc is dispensable for direct reprogramming of mouse fibroblasts
    • Wernig, M., Meissner, A., Cassady, J. P. & Jaenisch, R. c-Myc is dispensable for direct reprogramming of mouse fibroblasts. Cell Stem Cell 2, 10-12 (2008).
    • (2008) Cell Stem Cell , vol.2 , pp. 10-12
    • Wernig, M.1    Meissner, A.2    Cassady, J.P.3    Jaenisch, R.4
  • 44
    • 79960530899 scopus 로고    scopus 로고
    • Genomic imprinting: The emergence of an epigenetic paradigm
    • Ferguson-Smith, A. C. Genomic imprinting: the emergence of an epigenetic paradigm. Nat Rev Genet 12, 565-575 (2011).
    • (2011) Nat Rev Genet , vol.12 , pp. 565-575
    • Ferguson-Smith, A.C.1
  • 45
    • 35549001312 scopus 로고    scopus 로고
    • Genomic imprinting effects on brain development and function
    • DOI 10.1038/nrn2235, PII NRN2235
    • Wilkinson, L. S., Davies, W. & Isles, A. R. Genomic imprinting effects on brain development and function. Nature reviews. Neuroscience 8, 832-843 (2007). (Pubitemid 350006217)
    • (2007) Nature Reviews Neuroscience , vol.8 , Issue.11 , pp. 832-843
    • Wilkinson, L.S.1    Davies, W.2    Isles, A.R.3
  • 46
    • 57149092605 scopus 로고    scopus 로고
    • DNA methylation profile of tissue-dependent and differentially methylated regions (T-DMRs) in mouse promoter regions demonstrating tissuespecific gene expression
    • Yagi, S. et al. DNA methylation profile of tissue-dependent and differentially methylated regions (T-DMRs) in mouse promoter regions demonstrating tissuespecific gene expression. Genome Res 18, 1969-1978 (2008).
    • (2008) Genome Res , vol.18 , pp. 1969-1978
    • Yagi, S.1
  • 47
    • 77954504873 scopus 로고    scopus 로고
    • Conserved role of intragenic DNA methylation in regulating alternative promoters
    • Maunakea, A. K. et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature 466, 253-257 (2010).
    • (2010) Nature , vol.466 , pp. 253-257
    • Maunakea, A.K.1
  • 48
    • 79957925596 scopus 로고    scopus 로고
    • Accessible chromatin structure permits factors Sp1 and Sp3 to regulate human TGFBI gene expression
    • Lee, J. J. et al. Accessible chromatin structure permits factors Sp1 and Sp3 to regulate human TGFBI gene expression. Biochem Biophys Res Commun 409, 222-228 (2011).
    • (2011) Biochem Biophys Res Commun , vol.409 , pp. 222-228
    • Lee, J.J.1
  • 49
    • 58149182724 scopus 로고    scopus 로고
    • NCBIGEO: Archive for high-throughput functional genomic data
    • Barrett, T. et al.NCBIGEO: archive for high-throughput functional genomic data. Nucleic Acids Res 37, D885-890 (2009).
    • (2009) Nucleic Acids Res , vol.37
    • Barrett, T.1
  • 51
    • 44249093277 scopus 로고    scopus 로고
    • Expression analysis of G Protein-Coupled Receptors in mouse macrophages
    • Lattin, J. E. et al. Expression analysis of G Protein-Coupled Receptors in mouse macrophages. Immunome Res 4, 5 (2008).
    • (2008) Immunome Res , vol.4 , pp. 5
    • Lattin, J.E.1
  • 52
    • 0031178951 scopus 로고    scopus 로고
    • The mathematical theory of communication. 1963
    • Shannon, C. E. The mathematical theory of communication. 1963. MD Comput 14, 306-317 (1997).
    • (1997) MD Comput , vol.14 , pp. 306-317
    • Shannon, C.E.1
  • 53
    • 20044390368 scopus 로고    scopus 로고
    • DNA methylation profiling of the human major histocompatibility complex: A pilot study for the human epigenome project
    • Rakyan, V. K. et al. DNA methylation profiling of the human major histocompatibility complex: a pilot study for the human epigenome project. PLoS Biol 2, e405 (2004).
    • (2004) PLoS Biol , vol.2
    • Rakyan, V.K.1
  • 54
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang da, W., Sherman, B. T. & Lempicki, R. A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4, 44-57 (2009).
    • (2009) Nat Protoc , vol.4 , pp. 44-57
    • Huang Da, W.1    Sherman, B.T.2    Lempicki, R.A.3


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