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Volumn 6, Issue , 2015, Pages

Intermediate DNA methylation is a conserved signature of genome regulation

(24)  Elliott, Ginell a   Hong, Chibo b   Xing, Xiaoyun a   Zhou, Xin a   Li, Daofeng a   Coarfa, Cristian c   Bell, Robert J A b   Maire, Cecile L d   Ligon, Keith L d   Sigaroudinia, Mahvash e   Gascard, Philippe e   Tlsty, Thea D e   Harris, R Alan c   Schalkwyk, Leonard C f   Bilenky, Misha g   Mill, Jonathan h,i   Farnham, Peggy J j   Kellis, Manolis k   Marra, Marco A g   Milosavljevic, Aleksandar c   more..


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DEOXYRIBONUCLEASE I;

EID: 84923345958     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms7363     Document Type: Article
Times cited : (79)

References (45)
  • 1
    • 0033615717 scopus 로고    scopus 로고
    • DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development
    • Okano, M., Bell, D. W., Haber, D. a. & Li, E. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99, 247-257 (1999).
    • (1999) Cell , vol.99 , pp. 247-257
    • Okano, M.1    Bell, D.W.2    Haber, D.A.3    Li, E.4
  • 2
    • 70649095120 scopus 로고    scopus 로고
    • Differential methylation of tissue-and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts
    • Doi, A. et al. Differential methylation of tissue-and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts. Nature Genet. 41, 1350-1353 (2009).
    • (2009) Nature Genet. , vol.41 , pp. 1350-1353
    • Doi, A.1
  • 3
    • 79955777417 scopus 로고    scopus 로고
    • Genome-wide survey reveals dynamic widespread tissue-specific changes in DNA methylation during development
    • Liang, P. et al. Genome-wide survey reveals dynamic widespread tissue-specific changes in DNA methylation during development. BMC Genomics 12, 231 (2011).
    • (2011) BMC Genomics , vol.12 , pp. 231
    • Liang, P.1
  • 4
    • 79960688508 scopus 로고    scopus 로고
    • DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines
    • Bell, J. T. et al. DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. Genome Biol. 12, R10 (2011).
    • (2011) Genome Biol. , vol.12 , pp. R10
    • Bell, J.T.1
  • 5
    • 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
  • 6
    • 84875129831 scopus 로고    scopus 로고
    • DNA methylation dynamics in health and disease
    • Bergman, Y. & Cedar, H. DNA methylation dynamics in health and disease. Nat. Struct. Mol. Biol. 20, 274-281 (2013).
    • (2013) Nat. Struct. Mol. Biol. , vol.20 , pp. 274-281
    • Bergman, Y.1    Cedar, H.2
  • 7
    • 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
  • 8
    • 84883668746 scopus 로고    scopus 로고
    • Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm
    • Zhang, B. et al. Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm. Genome Res. 23, 1522-1540 (2013).
    • (2013) Genome Res. , vol.23 , pp. 1522-1540
    • Zhang, B.1
  • 9
    • 84885021247 scopus 로고    scopus 로고
    • Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues
    • Hon, G. C. et al. Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues. Nature Genet. 45, 1198-1206 (2013).
    • (2013) Nature Genet. , vol.45 , pp. 1198-1206
    • Hon, G.C.1
  • 10
    • 84882884517 scopus 로고    scopus 로고
    • Charting a dynamic DNA methylation landscape of the human genome
    • Ziller, M. J. et al. Charting a dynamic DNA methylation landscape of the human genome. Nature 500, 477-481 (2013).
    • (2013) Nature , vol.500 , pp. 477-481
    • Ziller, M.J.1
  • 11
    • 0027205671 scopus 로고
    • Allele-specific replication timing of imprinted gene regions
    • Kitsberg, D. et al. Allele-specific replication timing of imprinted gene regions. Nature 364, 459-463 (1993).
    • (1993) Nature , vol.364 , pp. 459-463
    • Kitsberg, D.1
  • 12
    • 0027172684 scopus 로고
    • Parental-origin-specific epigenetic modification of the mouse H19 gene
    • Ferguson-Smith, A. C., Sasaki, H., Cattanach, B. M. & Surani, M. A. Parental-origin-specific epigenetic modification of the mouse H19 gene. Nature 362, 751-755 (1993).
    • (1993) Nature , vol.362 , pp. 751-755
    • Ferguson-Smith, A.C.1    Sasaki, H.2    Cattanach, B.M.3    Surani, M.A.4
  • 13
    • 0030694713 scopus 로고    scopus 로고
    • Imprinted expression of the Igf2r gene depends on an intronic CpG island
    • Wutz, A. et al. Imprinted expression of the Igf2r gene depends on an intronic CpG island. Nature 389, 745-749 (1997).
    • (1997) Nature , vol.389 , pp. 745-749
    • Wutz, A.1
  • 14
    • 84857331867 scopus 로고    scopus 로고
    • Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation in the mouse genome
    • Xie, W. et al. Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation in the mouse genome. Cell 148, 816-831 (2012).
    • (2012) Cell , vol.148 , pp. 816-831
    • Xie, W.1
  • 15
    • 46249117780 scopus 로고    scopus 로고
    • Genomic surveys by methylation-sensitive SNP analysis identify sequence-dependent allele-specific DNA methylation
    • Kerkel, K. et al. Genomic surveys by methylation-sensitive SNP analysis identify sequence-dependent allele-specific DNA methylation. Nature Genet. 40, 904-908 (2008).
    • (2008) Nature Genet. , vol.40 , pp. 904-908
    • Kerkel, K.1
  • 16
    • 76049126281 scopus 로고    scopus 로고
    • Allelic skewing of DNA methylation is widespread across the genome
    • Schalkwyk, L. C. et al. Allelic skewing of DNA methylation is widespread across the genome. Am. J. Hum. Genet. 86, 196-212 (2010).
    • (2010) Am. J. Hum. Genet. , vol.86 , pp. 196-212
    • Schalkwyk, L.C.1
  • 17
    • 80052306947 scopus 로고    scopus 로고
    • Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation
    • Gertz, J. et al. Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation. PLoS Genet. 7, e1002228 (2011).
    • (2011) PLoS Genet. , vol.7
    • Gertz, J.1
  • 18
    • 84355163093 scopus 로고    scopus 로고
    • DNA-binding factors shape the mouse methylome at distal regulatory regions
    • Stadler, M. B. et al. DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature 480, 490-495 (2011).
    • (2011) Nature , vol.480 , pp. 490-495
    • Stadler, M.B.1
  • 19
    • 84861234288 scopus 로고    scopus 로고
    • Mechanisms and consequences of widespread random monoallelic expression
    • Chess, A. Mechanisms and consequences of widespread random monoallelic expression. Nat. Rev. Genet. 13, 421-428 (2012).
    • (2012) Nat. Rev. Genet. , vol.13 , pp. 421-428
    • Chess, A.1
  • 20
    • 84883719710 scopus 로고    scopus 로고
    • Estimating absolute methylation levels at single CpG resolution from methylation enrichment and restriction enzyme sequencing methods
    • Stevens, M. et al. Estimating absolute methylation levels at single CpG resolution from methylation enrichment and restriction enzyme sequencing methods. Genome Res. 23, 1541-1553 (2013).
    • (2013) Genome Res. , vol.23 , pp. 1541-1553
    • Stevens, M.1
  • 22
    • 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
  • 23
    • 77957932941 scopus 로고    scopus 로고
    • Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications
    • Harris, R. A. et al. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nature Biotechnol. 28, 1097-1105 (2010).
    • (2010) Nature Biotechnol. , vol.28 , pp. 1097-1105
    • Harris, R.A.1
  • 24
    • 84879611157 scopus 로고    scopus 로고
    • DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape
    • Xie, M. et al. DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape. Nature Genet. 45, 836-841 (2013).
    • (2013) Nature Genet. , vol.45 , pp. 836-841
    • Xie, M.1
  • 25
    • 84860808258 scopus 로고    scopus 로고
    • Genomic landscape of human allele-specific DNA methylation
    • Fang, F. et al. Genomic landscape of human allele-specific DNA methylation. Proc. Natl Acad. Sci. USA 109, 1-6 (2012).
    • (2012) Proc. Natl Acad. Sci. USA , vol.109 , pp. 1-6
    • Fang, F.1
  • 26
    • 83755224300 scopus 로고    scopus 로고
    • Significance analysis and statistical dissection of variably methylated regions
    • Jaffe, A. E., Feinberg, A. P., Irizarry, R. a. & Leek, J. T. Significance analysis and statistical dissection of variably methylated regions. Biostatistics 13, 166-178 (2012).
    • (2012) Biostatistics , vol.13 , pp. 166-178
    • Jaffe, A.E.1    Feinberg, A.P.2    Irizarry, R.A.3    Leek, J.T.4
  • 27
    • 84857707318 scopus 로고    scopus 로고
    • ChromHMM: Automating chromatin-state discovery and characterization
    • Ernst, J. & Kellis, M. ChromHMM: automating chromatin-state discovery and characterization. Nat. Methods 9, 215-216 (2012).
    • (2012) Nat. Methods , vol.9 , pp. 215-216
    • Ernst, J.1    Kellis, M.2
  • 28
    • 33846112470 scopus 로고    scopus 로고
    • VISTA Enhancer Browser - A database of tissue-specific human enhancers
    • Visel, A., Minovitsky, S., Dubchak, I. & Pennacchio, L. a. VISTA Enhancer Browser - a database of tissue-specific human enhancers. Nucleic Acids Res. 35, D88-D92 (2007).
    • (2007) Nucleic Acids Res. , vol.35 , pp. D88-D92
    • Visel, A.1    Minovitsky, S.2    Dubchak, I.3    Pennacchio, L.A.4
  • 29
    • 84870856116 scopus 로고    scopus 로고
    • Genome-wide DNA hydroxymethylation changes are associated with neurodevelopmental genes in the developing human cerebellum
    • Wang, T. et al. Genome-wide DNA hydroxymethylation changes are associated with neurodevelopmental genes in the developing human cerebellum. Hum. Mol. Genet 21, 5500-5510 (2012).
    • (2012) Hum. Mol. Genet , vol.21 , pp. 5500-5510
    • Wang, T.1
  • 30
    • 84887214395 scopus 로고    scopus 로고
    • Intragenic DNA methylation modulates alternative splicing by recruiting MeCP2 to promote exon recognition
    • Maunakea, A. K., Chepelev, I., Cui, K. & Zhao, K. Intragenic DNA methylation modulates alternative splicing by recruiting MeCP2 to promote exon recognition. Cell Res. 23, 1256-1269 (2013).
    • (2013) Cell Res. , vol.23 , pp. 1256-1269
    • Maunakea, A.K.1    Chepelev, I.2    Cui, K.3    Zhao, K.4
  • 31
    • 84890048526 scopus 로고    scopus 로고
    • Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins
    • Maeder, M. L. et al. Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins. Nature Biotechnol. 31, 1137-1142 (2013).
    • (2013) Nature Biotechnol. , vol.31 , pp. 1137-1142
    • Maeder, M.L.1
  • 32
    • 79959567069 scopus 로고    scopus 로고
    • Deterministic and stochastic allele specific gene expression in single mouse blastomeres
    • Tang, F. et al. Deterministic and stochastic allele specific gene expression in single mouse blastomeres. PLoS ONE 6, 11 (2011).
    • (2011) PLoS ONE , vol.6 , pp. 11
    • Tang, F.1
  • 33
    • 84878997106 scopus 로고    scopus 로고
    • Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells
    • Shalek, A. K. et al. Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. Nature 498, 236-240 (2013).
    • (2013) Nature , vol.498 , pp. 236-240
    • Shalek, A.K.1
  • 34
    • 84892179132 scopus 로고    scopus 로고
    • Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells
    • Deng, Q., Ramsköld, D., Reinius, B. & Sandberg, R. Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells. Science 343, 193-196 (2014).
    • (2014) Science , vol.343 , pp. 193-196
    • Deng, Q.1    Ramsköld, D.2    Reinius, B.3    Sandberg, R.4
  • 35
    • 79960927422 scopus 로고    scopus 로고
    • Increased methylation variation in epigenetic domains across cancer types
    • Hansen, K. D. et al. Increased methylation variation in epigenetic domains across cancer types. Nature Genet. 43, 768-775 (2011).
    • (2011) Nature Genet. , vol.43 , pp. 768-775
    • Hansen, K.D.1
  • 36
    • 80051967505 scopus 로고    scopus 로고
    • Stochastic state transitions give rise to phenotypic equilibrium in populations of cancer cells
    • Gupta, P. B. et al. Stochastic state transitions give rise to phenotypic equilibrium in populations of cancer cells. Cell 146, 633-644 (2011).
    • (2011) Cell , vol.146 , pp. 633-644
    • Gupta, P.B.1
  • 37
    • 77957940722 scopus 로고    scopus 로고
    • The NIH roadmap epigenomics mapping consortium
    • Bernstein, B. E. et al. The NIH Roadmap Epigenomics Mapping Consortium. Nature Biotechnol. 28, 1045-1048 (2010).
    • (2010) Nature Biotechnol. , vol.28 , pp. 1045-1048
    • Bernstein, B.E.1
  • 38
    • 0035252089 scopus 로고    scopus 로고
    • Normal human mammary epithelial cells spontaneously escape senescence and acquire genomic changes
    • Romanov, S. R. et al. Normal human mammary epithelial cells spontaneously escape senescence and acquire genomic changes. Nature 409, 633-637 (2001).
    • (2001) Nature , vol.409 , pp. 633-637
    • Romanov, S.R.1
  • 39
    • 43449130057 scopus 로고    scopus 로고
    • NS21: Re-defined and modified supplement B27 for neuronal cultures
    • Chen, Y. et al. NS21: re-defined and modified supplement B27 for neuronal cultures. J. Neurosci. Methods 171, 239-247 (2008).
    • (2008) J. Neurosci. Methods , vol.171 , pp. 239-247
    • Chen, Y.1
  • 40
    • 0242332183 scopus 로고    scopus 로고
    • Derepression of BDNF transcription involves calciumdependent phosphorylation of MeCP2
    • Chen, W. G. et al. Derepression of BDNF transcription involves calciumdependent phosphorylation of MeCP2. Science 302, 885-889 (2003).
    • (2003) Science , vol.302 , pp. 885-889
    • Chen, W.G.1
  • 41
    • 0035407651 scopus 로고    scopus 로고
    • Bisulfite genomic sequencing: Systematic investigation of critical experimental parameters
    • Grunau, C., Clark, S. J. & Rosenthal, A. Bisulfite genomic sequencing: systematic investigation of critical experimental parameters. Nucleic Acids Res. 29, E65-E65 (2001).
    • (2001) Nucleic Acids Res. , vol.29 , pp. E65-E65
    • Grunau, C.1    Clark, S.J.2    Rosenthal, A.3
  • 42
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: A flexible suite of utilities for comparing genomic features
    • Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 43
    • 34250305146 scopus 로고    scopus 로고
    • Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    • Consortium, E. P. et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799-816 (2007).
    • (2007) Nature , vol.447 , pp. 799-816
    • Consortium, E.P.1
  • 44
    • 0035173378 scopus 로고    scopus 로고
    • DbSNP: The NCBI database of genetic variation
    • Sherry, S. T. et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 29, 308-311 (2001).
    • (2001) Nucleic Acids Res. , vol.29 , pp. 308-311
    • Sherry, S.T.1


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