메뉴 건너뛰기




Volumn 32, Issue 19, 2016, Pages 2911-2919

AgIn: Measuring the landscape of CpG methylation of individual repetitive elements

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; CPG ISLAND; DNA METHYLATION; DNA SEQUENCE; HUMAN; HUMAN GENOME;

EID: 84990888281     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btw360     Document Type: Article
Times cited : (18)

References (54)
  • 1
    • 20344385787 scopus 로고    scopus 로고
    • Epigenetic transgenerational actions of endocrine disruptors and male fertility
    • Anway, M.D. et al. (2005) Epigenetic transgenerational actions of endocrine disruptors and male fertility. Science, 308, 1466-1469.
    • (2005) Science , vol.308 , pp. 1466-1469
    • Anway, M.D.1
  • 2
    • 84863664355 scopus 로고    scopus 로고
    • A hybrid approach for the automated finishing of bacterial genomes
    • Bashir, A. et al. (2012) A hybrid approach for the automated finishing of bacterial genomes. Nat. Biotechnol., 30, 701-707.
    • (2012) Nat. Biotechnol. , vol.30 , pp. 701-707
    • Bashir, A.1
  • 3
    • 77953880842 scopus 로고    scopus 로고
    • LINE-1 retrotransposition activity in human genomes
    • Beck, C.R. et al. (2010) LINE-1 retrotransposition activity in human genomes. Cell, 141, 1159-1170.
    • (2010) Cell , vol.141 , pp. 1159-1170
    • Beck, C.R.1
  • 4
    • 84921766043 scopus 로고    scopus 로고
    • Detecting epigenetic motifs in low coverage and metagenomics settings
    • Beckmann, N.D. et al. (2014) Detecting epigenetic motifs in low coverage and metagenomics settings. BMC Bioinformatics, 15, S16.
    • (2014) BMC Bioinformatics , vol.15 , pp. S16
    • Beckmann, N.D.1
  • 5
    • 45549096818 scopus 로고    scopus 로고
    • Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping
    • Bock, C. et al. (2008) Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping. Nucleic Acids Res., 36, e55.
    • (2008) Nucleic Acids Res. , vol.36 , pp. e55
    • Bock, C.1
  • 6
    • 84861802222 scopus 로고    scopus 로고
    • Direct detection and sequencing of damaged DNA bases
    • Clark, T.A. et al. (2011) Direct detection and sequencing of damaged DNA bases. Genome Integrity, 2, 10.
    • (2011) Genome Integrity , vol.2 , pp. 10
    • Clark, T.A.1
  • 7
    • 84857877933 scopus 로고    scopus 로고
    • Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing
    • Clark, T.A. et al. (2012) Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing. Nucleic Acids Res., 40, e29.
    • (2012) Nucleic Acids Res. , vol.40 , pp. e29
    • Clark, T.A.1
  • 8
    • 84872450066 scopus 로고    scopus 로고
    • Enhanced 5-methylcytosine detection in single-molecule, real-time sequencing via tet1 oxidation
    • Clark, T. et al. (2013) Enhanced 5-methylcytosine detection in single-molecule, real-time sequencing via tet1 oxidation. BMC Biology, 11, 4.
    • (2013) BMC Biology , vol.11 , pp. 4
    • Clark, T.1
  • 9
    • 40749109894 scopus 로고    scopus 로고
    • Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning
    • Cokus, S.J. et al. (2008) Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature, 452, 215-219.
    • (2008) Nature , vol.452 , pp. 215-219
    • Cokus, S.J.1
  • 10
    • 0024342297 scopus 로고
    • Cytosine methylation and the fate of CpG dinucleotides in vertebrate genomes
    • Cooper, D. and Krawczak, M. (1989) Cytosine methylation and the fate of CpG dinucleotides in vertebrate genomes. Hum. Genet., 83, 181.
    • (1989) Hum. Genet. , vol.83 , pp. 181
    • Cooper, D.1    Krawczak, M.2
  • 12
    • 33751505540 scopus 로고    scopus 로고
    • DNA methylation profiling of human chromosomes 6, 20 and 22
    • Eckhardt, F. et al. (2006) DNA methylation profiling of human chromosomes 6, 20 and 22. Nat. Genet., 38, 1378-1385.
    • (2006) Nat. Genet. , vol.38 , pp. 1378-1385
    • Eckhardt, F.1
  • 13
    • 58149234737 scopus 로고    scopus 로고
    • Real-time DNA sequencing from single polymerase molecules
    • Eid, J. et al. (2009) Real-time DNA sequencing from single polymerase molecules. Science (New York, N.Y.), 323, 133-138.
    • (2009) Science (New York, N.Y.) , vol.323 , pp. 133-138
    • Eid, J.1
  • 14
    • 84869814079 scopus 로고    scopus 로고
    • Mind the gap: Upgrading genomes with pacific bio-sciences RS long-read sequencing technology
    • English, A.C. et al. (2012) Mind the gap: upgrading genomes with pacific bio-sciences RS long-read sequencing technology. PLoS ONE, 7, e47768.
    • (2012) PLoS ONE , vol.7 , pp. e47768
    • English, A.C.1
  • 15
    • 84870880581 scopus 로고    scopus 로고
    • Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing
    • Fang, G. et al. (2012) Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing. Nat. Biotechnol, 30, 1232-1239.
    • (2012) Nat. Biotechnol , vol.30 , pp. 1232-1239
    • Fang, G.1
  • 16
    • 84875981516 scopus 로고    scopus 로고
    • Detecting DNA modifications from SMRT sequencing data by modeling sequence context dependence of polymerase kinetic
    • Feng, Z. et al. (2013) Detecting DNA modifications from SMRT sequencing data by modeling sequence context dependence of polymerase kinetic. PLoS Comput. Biol., 9, e1002935.
    • (2013) PLoS Comput. Biol. , vol.9 , pp. e1002935
    • Feng, Z.1
  • 17
    • 77952967431 scopus 로고    scopus 로고
    • Direct detection of DNA methylation during single-molecule, real-time sequencing
    • Flusberg, B.A. et al. (2010) Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat. Methods, 7, 461-465.
    • (2010) Nat. Methods , vol.7 , pp. 461-465
    • Flusberg, B.A.1
  • 18
    • 0033631415 scopus 로고    scopus 로고
    • The biological properties and evolutionary dynamics of mammalian line-1 retrotransposons
    • Furano, A. (2000) The biological properties and evolutionary dynamics of mammalian line-1 retrotransposons. Prog. Nucleic Acid Res. Mol. Biol., 64, 255-294.
    • (2000) Prog. Nucleic Acid Res. Mol. Biol. , vol.64 , pp. 255-294
    • Furano, A.1
  • 19
    • 84878292277 scopus 로고    scopus 로고
    • Transcriptional and epigenetic dynamics during specification of human embryonic stem cells
    • Gifford, C.A. et al. (2013) Transcriptional and epigenetic dynamics during specification of human embryonic stem cells. Cell, 153, 1149-1163.
    • (2013) Cell , vol.153 , pp. 1149-1163
    • Gifford, C.A.1
  • 20
    • 84899482147 scopus 로고    scopus 로고
    • Retrotransposition in tumors and brains
    • Goodier, J.L. (2014) Retrotransposition in tumors and brains. Mobile DNA, 5, 11.
    • (2014) Mobile DNA , vol.5 , pp. 11
    • Goodier, J.L.1
  • 21
    • 84937012244 scopus 로고    scopus 로고
    • DNA methylation on n 6-adenine in C. elegans
    • Greer, E.L. et al. (2015) DNA methylation on n 6-adenine in C. elegans. Cell, 161, 868-878.
    • (2015) Cell , vol.161 , pp. 868-878
    • Greer, E.L.1
  • 22
    • 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. (2010) Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat. Biotechnol., 28, 1097-1105.
    • (2010) Nat. Biotechnol. , vol.28 , pp. 1097-1105
    • Harris, R.A.1
  • 23
    • 33745628063 scopus 로고    scopus 로고
    • Targeted reduction of the DNA methylation level with 5-azacytidine promotes excision of the medaka fish Tol2 transposable element
    • Iida, A. et al. (2006) Targeted reduction of the DNA methylation level with 5-azacytidine promotes excision of the medaka fish Tol2 transposable element. Genet. Res., 87, 187-193.
    • (2006) Genet. Res. , vol.87 , pp. 187-193
    • Iida, A.1
  • 24
    • 38449110499 scopus 로고    scopus 로고
    • Tol2: A versatile gene transfer vector in vertebrates
    • Kawakami, K. (2007) Tol2: a versatile gene transfer vector in vertebrates. Genome Biol., 8, 1-10.
    • (2007) Genome Biol. , vol.8 , pp. 1-10
    • Kawakami, K.1
  • 25
    • 0034060756 scopus 로고    scopus 로고
    • Evidence for recent invasion of the medaka fish genome by the tol2 transposable element
    • Koga, A. et al. (2000) Evidence for recent invasion of the medaka fish genome by the tol2 transposable element. Genetics, 155, 273.
    • (2000) Genetics , vol.155 , pp. 273
    • Koga, A.1
  • 26
    • 84863651532 scopus 로고    scopus 로고
    • Hybrid error correction and de novo assembly of single-molecule sequencing reads
    • Koren, S. et al. (2012) Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat. Biotechnol., 30, 693-700.
    • (2012) Nat. Biotechnol. , vol.30 , pp. 693-700
    • Koren, S.1
  • 27
    • 39549114616 scopus 로고    scopus 로고
    • Selective aluminum passivation for targeted immobilization of single DNA polymerase molecules in zero-mode waveguide nano-structures
    • Korlach, J. et al. (2008) Selective aluminum passivation for targeted immobilization of single DNA polymerase molecules in zero-mode waveguide nano-structures. Proc. Natl Acad. Sci. U. S. A., 105, 1176-1181.
    • (2008) Proc. Natl Acad. Sci. U. S. A. , vol.105 , pp. 1176-1181
    • Korlach, J.1
  • 28
    • 84865285978 scopus 로고    scopus 로고
    • Landscape of somatic retrotransposition in human cancers
    • Lee, E. et al. (2012) Landscape of somatic retrotransposition in human cancers. Science, 337, 967-971.
    • (2012) Science , vol.337 , pp. 967-971
    • Lee, E.1
  • 29
    • 42749087226 scopus 로고    scopus 로고
    • Highly integrated single-base resolution maps of the epi-genome in Arabidopsis
    • Lister, R. et al. (2008) Highly integrated single-base resolution maps of the epi-genome in Arabidopsis. Cell, 133, 523-536.
    • (2008) Cell , vol.133 , pp. 523-536
    • Lister, R.1
  • 30
    • 70450217879 scopus 로고    scopus 로고
    • Human DNA methylomes at base resolution show widespread epigenomic differences
    • Lister, R. et al. (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature, 462, 315-322.
    • (2009) Nature , vol.462 , pp. 315-322
    • Lister, R.1
  • 31
    • 84871392152 scopus 로고    scopus 로고
    • Sequencing the unsequenceable: Expanded CGG-repeat alleles of the fragile x gene
    • Loomis, E.W. et al. (2012) Sequencing the unsequenceable: expanded CGG-repeat alleles of the fragile x gene. Genome Res., 23, 121-128.
    • (2012) Genome Res. , vol.23 , pp. 121-128
    • Loomis, E.W.1
  • 32
    • 49649125042 scopus 로고    scopus 로고
    • Genome-scale DNA methylation maps of pluripotent and differentiated cells
    • Meissner, A. et al. (2008) Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature, 454, 766-770.
    • (2008) Nature , vol.454 , pp. 766-770
    • Meissner, A.1
  • 33
    • 77954324820 scopus 로고    scopus 로고
    • Epigenetics the seductive allure of behavioral epigenetics
    • Miller, G. (2010) Epigenetics. The seductive allure of behavioral epigenetics. Science, 329, 24-27.
    • (2010) Science , vol.329 , pp. 24-27
    • Miller, G.1
  • 34
    • 84866919003 scopus 로고    scopus 로고
    • Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging
    • Miura, F. et al. (2012) Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging. Nucleic Acids Res., 40, e136-e136.
    • (2012) Nucleic Acids Res. , vol.40 , pp. e136-e136
    • Miura, F.1
  • 35
    • 80052937538 scopus 로고    scopus 로고
    • Sperm methylation profiles reveal features of epigen-etic inheritance and evolution in primates
    • Molaro, A. et al. (2011) Sperm methylation profiles reveal features of epigen-etic inheritance and evolution in primates. Cell, 146, 1029-1041.
    • (2011) Cell , vol.146 , pp. 1029-1041
    • Molaro, A.1
  • 36
    • 20544466648 scopus 로고    scopus 로고
    • Somatic mosaicism in neuronal precursor cells mediated by L1 retrotransposition
    • Muotri, A.R. et al. (2005) Somatic mosaicism in neuronal precursor cells mediated by L1 retrotransposition. Nature, 435, 903-910.
    • (2005) Nature , vol.435 , pp. 903-910
    • Muotri, A.R.1
  • 37
    • 78549247463 scopus 로고    scopus 로고
    • L1 retrotransposition in neurons is modulated by mecp2
    • Muotri, A.R. et al. (2010) L1 retrotransposition in neurons is modulated by mecp2. Nature, 468, 443-446.
    • (2010) Nature , vol.468 , pp. 443-446
    • Muotri, A.R.1
  • 38
    • 77955458087 scopus 로고    scopus 로고
    • High-throughput method for analyzing methylation of CpGs in targeted genomic regions
    • Nautiyal, S. et al. (2010) High-throughput method for analyzing methylation of CpGs in targeted genomic regions. Proc. Natl Acad. Sci. U. S. A., 107, 12587-12592.
    • (2010) Proc. Natl Acad. Sci. U. S. A. , vol.107 , pp. 12587-12592
    • Nautiyal, S.1
  • 39
    • 13444282428 scopus 로고    scopus 로고
    • L1base: From functional annotation to prediction of active line-1 elements
    • Penzkofer, T. et al. (2005) L1base: from functional annotation to prediction of active line-1 elements. Nucleic Acids Res., 33, D498-D500.
    • (2005) Nucleic Acids Res. , vol.33 , pp. D498-D500
    • Penzkofer, T.1
  • 40
    • 84864634108 scopus 로고    scopus 로고
    • Genome-wide genetic variations are highly correlated with proximal DNA methylation patterns
    • Qu, W. et al. (2012) Genome-wide genetic variations are highly correlated with proximal DNA methylation patterns. Genome Res., 22, 1419-1425.
    • (2012) Genome Res. , vol.22 , pp. 1419-1425
    • Qu, W.1
  • 41
    • 77954137460 scopus 로고    scopus 로고
    • Hypomethylation of repeated DNA sequences in cancer
    • Ross, J.P. et al. (2010) Hypomethylation of repeated DNA sequences in cancer. Epigenomics, 2, 245-269.
    • (2010) Epigenomics , vol.2 , pp. 245-269
    • Ross, J.P.1
  • 42
    • 84870939871 scopus 로고    scopus 로고
    • Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases
    • Schadt, E.E. et al. (2012) Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases. Genome Res., 23, 129-141.
    • (2012) Genome Res. , vol.23 , pp. 129-141
    • Schadt, E.E.1
  • 43
    • 80054837794 scopus 로고    scopus 로고
    • Transgenerational epigenetic instability is a source of novel methylation variants
    • Schmitz, R.J. et al. (2011) Transgenerational epigenetic instability is a source of novel methylation variants. Science (New York, N.Y.), 334, 369-373.
    • (2011) Science (New York, N.Y.) , vol.334 , pp. 369-373
    • Schmitz, R.J.1
  • 44
    • 77954238686 scopus 로고    scopus 로고
    • Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome
    • Shoemaker, R. et al. (2010) Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome. Genome Res., 20, 883-889.
    • (2010) Genome Res. , vol.20 , pp. 883-889
    • Shoemaker, R.1
  • 45
    • 84859910536 scopus 로고    scopus 로고
    • A unique regulatory phase of DNA methylation in the early mammalian embryo
    • Smith, Z.D. et al. (2012) A unique regulatory phase of DNA methylation in the early mammalian embryo. Nature, 484, 339-344.
    • (2012) Nature , vol.484 , pp. 339-344
    • Smith, Z.D.1
  • 46
    • 84871799766 scopus 로고    scopus 로고
    • CpG-mps: Identification of CpG methylation patterns of genomic regions from high-throughput bisulfite sequencing data
    • Su, J. et al. (2012) CpG-mps: identification of CpG methylation patterns of genomic regions from high-throughput bisulfite sequencing data. Nucleic Acids Res, 41, e4.
    • (2012) Nucleic Acids Res , vol.41 , pp. e4
    • Su, J.1
  • 47
    • 84905900534 scopus 로고    scopus 로고
    • Extensive transduction of nonrepetitive DNA mediated by l1 retrotransposition in cancer genomes
    • Tubio, J.M.C. et al. (2014) Extensive transduction of nonrepetitive DNA mediated by l1 retrotransposition in cancer genomes. Science, 345, 1251343.
    • (2014) Science , vol.345 , pp. 1251343
    • Tubio, J.M.C.1
  • 48
    • 84943756057 scopus 로고    scopus 로고
    • A systematic study of normalization methods for Infinium 450 K methylation data using whole-genome bisulfite sequencing data
    • Wang, T. et al. (2015) A systematic study of normalization methods for Infinium 450 K methylation data using whole-genome bisulfite sequencing data. Epigenetics, 10, 662-669.
    • (2015) Epigenetics , vol.10 , pp. 662-669
    • Wang, T.1
  • 49
    • 3342989681 scopus 로고    scopus 로고
    • Epigenetic programming by maternal behavior
    • Weaver, I.C. et al. (2004) Epigenetic programming by maternal behavior. Nat. Neurosci., 7, 847-854.
    • (2004) Nat. Neurosci. , vol.7 , pp. 847-854
    • Weaver, I.C.1
  • 50
    • 33845332711 scopus 로고    scopus 로고
    • DNA hypomethylation and human diseases
    • Wilson, A.S. et al. (2007) DNA hypomethylation and human diseases. Biochim. Biophys. Acta, 1775, 138-162.
    • (2007) Biochim. Biophys. Acta , vol.1775 , pp. 138-162
    • Wilson, A.S.1
  • 51
    • 84878282421 scopus 로고    scopus 로고
    • Epigenomic analysis of multilineage differentiation of human embryonic stem cells
    • Xie, W. et al. (2013) Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell, 153, 1134-1148.
    • (2013) Cell , vol.153 , pp. 1134-1148
    • Xie, W.1
  • 52
    • 84928812813 scopus 로고    scopus 로고
    • Quantitative and multiplexed DNA methylation analysis using long-read single-molecule real-time bisulfite sequencing (SMRT-BS)
    • Yang, Y. et al. (2015) Quantitative and multiplexed DNA methylation analysis using long-read single-molecule real-time bisulfite sequencing (SMRT-BS). BMC Genomics, 16, 350.
    • (2015) BMC Genomics , vol.16 , pp. 350
    • Yang, Y.1
  • 53
    • 77952355762 scopus 로고    scopus 로고
    • Genome-wide evolutionary analysis of eukaryotic DNA methylation
    • Zemach, A. et al. (2010) Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science, 328, 916-919.
    • (2010) Science , vol.328 , pp. 916-919
    • Zemach, A.1
  • 54
    • 84863886793 scopus 로고    scopus 로고
    • Improving genome assemblies by sequencing PCR products with PacBio
    • Zhang, X. et al. (2012) Improving genome assemblies by sequencing PCR products with PacBio. BioTechniques, 53, 61-62.
    • (2012) BioTechniques , vol.53 , pp. 61-62
    • Zhang, X.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.