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Volumn 27, Issue 1, 2017, Pages 118-132

The epigenetic landscape of Alu repeats delineates the structural and functional genomic architecture of colon cancer cells

Author keywords

[No Author keywords available]

Indexed keywords

ALU SEQUENCE; ARTICLE; BISULFITE SEQUENCING; CANCER CELL; CHROMOSOMAL INSTABILITY; COLORECTAL CANCER; CONTROLLED STUDY; DNA METHYLATION; DNA REPLICATION; EPIGENETICS; GENE DOSAGE; GENOME ANALYSIS; HUMAN; HUMAN CELL; HUMAN TISSUE; NEXT GENERATION SEQUENCING; NEXT GENERATION SEQUENCING OF UNMETHYLATED ALU; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RETROPOSON; SEQUENCE ANALYSIS; TRANSCRIPTOMICS; COLON TUMOR; CPG ISLAND; GENETIC EPIGENESIS; GENETICS; GENOMICS; HIGH THROUGHPUT SEQUENCING; HUMAN GENOME;

EID: 85009115714     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.207522.116     Document Type: Article
Times cited : (46)

References (113)
  • 1
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • Anders S, Huber W. 2010. Differential expression analysis for sequence count data. Genome Biol 11: R106.
    • (2010) Genome Biol , vol.11 , pp. R106
    • Anders, S.1    Huber, W.2
  • 2
    • 84961202658 scopus 로고    scopus 로고
    • DNA methylation variation of human-specific Alu repeats
    • Bakshi A, Herke S, Batzer MA, Kim J. 2016. DNA methylation variation of human-specific Alu repeats. Epigenetics 11: 163-173.
    • (2016) Epigenetics , vol.11 , pp. 163-173
    • Bakshi, A.1    Herke, S.2    Batzer, M.A.3    Kim, J.4
  • 3
    • 84871194526 scopus 로고    scopus 로고
    • Evaluation of single CpG sites as proxies of CpG island methylation states at the genome scale
    • Barrera V, Peinado MA. 2012. Evaluation of single CpG sites as proxies of CpG island methylation states at the genome scale. Nucleic Acids Res 40: 11490-11498.
    • (2012) Nucleic Acids Res , vol.40 , pp. 11490-11498
    • Barrera, V.1    Peinado, M.A.2
  • 4
    • 77957948773 scopus 로고    scopus 로고
    • Taking the measure of the methylome
    • Beck S. 2010. Taking the measure of the methylome. Nat Biotechnol 28: 1026-1028.
    • (2010) Nat Biotechnol , vol.28 , pp. 1026-1028
    • Beck, S.1
  • 8
    • 0036144048 scopus 로고    scopus 로고
    • DNA methylation patterns and epigenetic memory
    • Bird A. 2002. DNA methylation patterns and epigenetic memory. Genes Dev 16: 6-21.
    • (2002) Genes Dev , vol.16 , pp. 6-21
    • Bird, A.1
  • 10
    • 85044707152 scopus 로고    scopus 로고
    • Interview with Sydney Brenner by Soraya de Chadarevian
    • Brenner S. 2009. Interview with Sydney Brenner by Soraya de Chadarevian. Stud Hist Philos Biol Biomed Sci 40: 65-71.
    • (2009) Stud Hist Philos Biol Biomed Sci , vol.40 , pp. 65-71
    • Brenner, S.1
  • 11
    • 33645744394 scopus 로고    scopus 로고
    • Evolutionary evidence suggests that CpG islandassociated Alus are frequently unmethylated in human germline
    • Brohede J, Rand KN. 2006. Evolutionary evidence suggests that CpG islandassociated Alus are frequently unmethylated in human germline. Hum Genet 119: 457-458.
    • (2006) Hum Genet , vol.119 , pp. 457-458
    • Brohede, J.1    Rand, K.N.2
  • 14
    • 0037022569 scopus 로고    scopus 로고
    • Genes, pseudogenes, and Alu sequence organization across human chromosomes 21 and 22
    • Chen C, Gentles AJ, Jurka J, Karlin S. 2002. Genes, pseudogenes, and Alu sequence organization across human chromosomes 21 and 22. Proc Natl Acad Sci 99: 2930-2935.
    • (2002) Proc Natl Acad Sci , vol.99 , pp. 2930-2935
    • Chen, C.1    Gentles, A.J.2    Jurka, J.3    Karlin, S.4
  • 15
    • 34250645744 scopus 로고    scopus 로고
    • Hypomethylation of LINE-1 and Alu in well-differentiated neuroendocrine tumors (pancreatic endocrine tumors and carcinoid tumors)
    • Choi IS, Estecio MR, Nagano Y, Kim do H, White JA, Yao JC, Issa JP, Rashid A. 2007. Hypomethylation of LINE-1 and Alu in well-differentiated neuroendocrine tumors (pancreatic endocrine tumors and carcinoid tumors). Mod Pathol 20: 802-810.
    • (2007) Mod Pathol , vol.20 , pp. 802-810
    • Choi, I.S.1    Estecio, M.R.2    Nagano, Y.3    Do Kim, H.4    White, J.A.5    Yao, J.C.6    Issa, J.P.7    Rashid, A.8
  • 16
  • 17
    • 70349318211 scopus 로고    scopus 로고
    • The impact of retrotransposons on human genome evolution
    • Cordaux R, Batzer MA. 2009. The impact of retrotransposons on human genome evolution. Nat Rev Genet 10: 691-703.
    • (2009) Nat Rev Genet , vol.10 , pp. 691-703
    • Cordaux, R.1    Batzer, M.A.2
  • 18
    • 78650855113 scopus 로고    scopus 로고
    • Impact of Alu repeats on the evolution of human p53 binding sites
    • Cui F, SirotinMV, Zhurkin VB. 2011. Impact of Alu repeats on the evolution of human p53 binding sites. Biol Direct 6: 2.
    • (2011) Biol Direct , vol.6 , pp. 2
    • Cui, F.1    Sirotin, M.V.2    Zhurkin, V.B.3
  • 19
    • 84944155589 scopus 로고    scopus 로고
    • The role of Alu elements in the cis-regulation of RNA processing
    • Daniel C, Behm M, Öhman M. 2015. The role of Alu elements in the cis-regulation of RNA processing. Cell Mol Life Sci 72: 4063-4076.
    • (2015) Cell Mol Life Sci , vol.72 , pp. 4063-4076
    • Daniel, C.1    Behm, M.2    Öhman, M.3
  • 20
    • 84855199454 scopus 로고    scopus 로고
    • Alu elements: Know the SINEs
    • Deininger P. 2011. Alu elements: Know the SINEs. Genome Biol 12: 236.
    • (2011) Genome Biol , vol.12 , pp. 236
    • Deininger, P.1
  • 21
    • 84878011578 scopus 로고    scopus 로고
    • Exploring the three-dimensional organization of genomes: Interpreting chromatin interaction data
    • Dekker J, Marti-Renom MA, Mirny LA. 2013. Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nat Rev Genet 14: 390-403.
    • (2013) Nat Rev Genet , vol.14 , pp. 390-403
    • Dekker, J.1    Marti-Renom, M.A.2    Mirny, L.A.3
  • 22
    • 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
    • Doi A, Park IH, Wen B, Murakami P, Aryee MJ, Irizarry R, Herb B, Ladd-Acosta C, Rho J, Loewer S, et al. 2009. Differential methylation of tissueand cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts. Nat Genet 41: 1350-1353.
    • (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    Herb, B.7    Ladd-Acosta, C.8    Rho, J.9    Loewer, S.10
  • 23
    • 84951325892 scopus 로고    scopus 로고
    • Competition betweenDNA methylation and transcription factors determines binding of NRF1
    • Domcke S, Bardet AF, Adrian Ginno P, Hartl D, Burger L, Schübeler D. 2015. Competition betweenDNA methylation and transcription factors determines binding of NRF1. Nature 528: 575-579.
    • (2015) Nature , vol.528 , pp. 575-579
    • Domcke, S.1    Bardet, A.F.2    Adrian Ginno, P.3    Hartl, D.4    Burger, L.5    Schübeler, D.6
  • 24
    • 0242584454 scopus 로고    scopus 로고
    • Chromosomal instability and tumors promoted by DNA hypomethylation
    • Eden A, Gaudet F, Waghmare A, Jaenisch R. 2003. Chromosomal instability and tumors promoted by DNA hypomethylation. Science 300: 455.
    • (2003) Science , vol.300 , pp. 455
    • Eden, A.1    Gaudet, F.2    Waghmare, A.3    Jaenisch, R.4
  • 26
    • 77954661906 scopus 로고    scopus 로고
    • DNA hypomethylation in cancer cells
    • Ehrlich M. 2009. DNA hypomethylation in cancer cells. Epigenomics 1: 239-259.
    • (2009) Epigenomics , vol.1 , pp. 239-259
    • Ehrlich, M.1
  • 28
    • 0028951144 scopus 로고
    • Nucleosome positioning by human Alu elements in chromatin
    • Englander EW, Howard BH. 1995. Nucleosome positioning by human Alu elements in chromatin. J Biol Chem 270: 10091-10096.
    • (1995) J Biol Chem , vol.270 , pp. 10091-10096
    • Englander, E.W.1    Howard, B.H.2
  • 29
    • 78650747491 scopus 로고    scopus 로고
    • Discovery and characterization of chromatin states for systematic annotation of the human genome
    • Ernst J, Kellis M. 2010. Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol 28: 817-825.
    • (2010) Nat Biotechnol , vol.28 , pp. 817-825
    • Ernst, J.1    Kellis, M.2
  • 30
    • 33947315736 scopus 로고    scopus 로고
    • Cancer epigenomics: DNA methylomes and histone-modification maps
    • Esteller M. 2007. Cancer epigenomics: DNA methylomes and histone-modification maps. Nat Rev Genet 8: 286-298.
    • (2007) Nat Rev Genet , vol.8 , pp. 286-298
    • Esteller, M.1
  • 31
    • 40849139208 scopus 로고    scopus 로고
    • Epigenetics in cancer
    • Esteller M. 2008. Epigenetics in cancer. N Engl J Med 358: 1148-1159.
    • (2008) N Engl J Med , vol.358 , pp. 1148-1159
    • Esteller, M.1
  • 32
    • 1042278765 scopus 로고    scopus 로고
    • The history of cancer epigenetics
    • Feinberg AP, Tycko B. 2004. The history of cancer epigenetics. Nat Rev Cancer 4: 143-153.
    • (2004) Nat Rev Cancer , vol.4 , pp. 143-153
    • Feinberg, A.P.1    Tycko, B.2
  • 33
    • 84961218734 scopus 로고    scopus 로고
    • Disease mechanisms: Epigenetic modulators, modifiers and mediators in cancer aetiology and progression
    • Feinberg AP, Koldobskiy MA, Gondor A. 2016. Disease mechanisms: epigenetic modulators, modifiers and mediators in cancer aetiology and progression. Nat Rev Genet 17: 284-299.
    • (2016) Nat Rev Genet , vol.17 , pp. 284-299
    • Feinberg, A.P.1    Koldobskiy, M.A.2    Gondor, A.3
  • 34
    • 84887990323 scopus 로고    scopus 로고
    • Long range epigenetic silencing is a transspecies mechanism that results in cancer specific deregulation by overriding the chromatin domains of normal cells
    • Forn M, Muñoz M, Tauriello DV, Merlos-Suárez A, Rodilla V, Bigas A, Batlle E, Jordà M, Peinado MA. 2013. Long range epigenetic silencing is a transspecies mechanism that results in cancer specific deregulation by overriding the chromatin domains of normal cells. Mol Oncol 7: 1129-1141.
    • (2013) Mol Oncol , vol.7 , pp. 1129-1141
    • Forn, M.1    Muñoz, M.2    Tauriello, D.V.3    Merlos-Suárez, A.4    Rodilla, V.5    Bigas, A.6    Batlle, E.7    Jordà, M.8    Peinado, M.A.9
  • 35
    • 33646369393 scopus 로고    scopus 로고
    • Epigenetic remodeling in colorectal cancer results in coordinate gene suppression across an entire chromosome band
    • Frigola J, Song J, Stirzaker C, Hinshelwood RA, Peinado MA, Clark S. 2006. Epigenetic remodeling in colorectal cancer results in coordinate gene suppression across an entire chromosome band. Nat Genet 38: 540-549.
    • (2006) Nat Genet , vol.38 , pp. 540-549
    • Frigola, J.1    Song, J.2    Stirzaker, C.3    Hinshelwood, R.A.4    Peinado, M.A.5    Clark, S.6
  • 36
    • 84860174658 scopus 로고    scopus 로고
    • ComprehensiveDNA methylation profiling of human repetitive DNA elements using an MeDIP-on-RepArray assay
    • Gilson E, Horard B. 2012. ComprehensiveDNA methylation profiling of human repetitive DNA elements using an MeDIP-on-RepArray assay. Methods Mol Biol 859: 267-291.
    • (2012) Methods Mol Biol , vol.859 , pp. 267-291
    • Gilson, E.1    Horard, B.2
  • 37
    • 15744401773 scopus 로고    scopus 로고
    • Eukaryotic cytosine methyltransferases
    • Goll MG, Bestor TH. 2005. Eukaryotic cytosine methyltransferases. Annu Rev Biochem 74: 481-514.
    • (2005) Annu Rev Biochem , vol.74 , pp. 481-514
    • Goll, M.G.1    Bestor, T.H.2
  • 38
    • 84921443442 scopus 로고    scopus 로고
    • Architectural proteins: Regulators of 3D genome organization in cell fate
    • Gómez-Díaz E, Corces VG. 2014. Architectural proteins: regulators of 3D genome organization in cell fate. Trends Cell Biol 24: 703-711.
    • (2014) Trends Cell Biol , vol.24 , pp. 703-711
    • Gómez-Díaz, E.1    Corces, V.G.2
  • 40
    • 2342437120 scopus 로고    scopus 로고
    • Alu repeat analysis in the complete human genome: Trends and variations with respect to genomic composition
    • Grover D, Mukerji M, Bhatnagar P, Kannan K, Brahmachari SK. 2004. Alu repeat analysis in the complete human genome: trends and variations with respect to genomic composition. Bioinformatics 20: 813-817.
    • (2004) Bioinformatics , vol.20 , pp. 813-817
    • Grover, D.1    Mukerji, M.2    Bhatnagar, P.3    Kannan, K.4    Brahmachari, S.K.5
  • 46
    • 33751012428 scopus 로고    scopus 로고
    • Alu elements as regulators of gene expression
    • Häsler J, Strub K. 2006. Alu elements as regulators of gene expression. Nucleic Acids Res 34: 5491-5497.
    • (2006) Nucleic Acids Res , vol.34 , pp. 5491-5497
    • Häsler, J.1    Strub, K.2
  • 49
    • 84877910548 scopus 로고    scopus 로고
    • Epigenetic regulation of transcription and possible functions of mammalian short interspersed elements, SINEs
    • Ichiyanagi K. 2013. Epigenetic regulation of transcription and possible functions of mammalian short interspersed elements, SINEs. Genes Genet Syst 88: 19-29.
    • (2013) Genes Genet Syst , vol.88 , pp. 19-29
    • Ichiyanagi, K.1
  • 50
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing and analysis of the human genome
    • International Human Genome Sequencing Consortium
    • International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature 409: 860-921.
    • (2001) Nature , vol.409 , pp. 860-921
  • 52
    • 2542449016 scopus 로고    scopus 로고
    • Repetitive sequences that shape the human transcriptome
    • Jasinska A, Krzyzosiak WJ. 2004. Repetitive sequences that shape the human transcriptome. FEBS Lett 567: 136-141.
    • (2004) FEBS Lett , vol.567 , pp. 136-141
    • Jasinska, A.1    Krzyzosiak, W.J.2
  • 53
    • 77951169806 scopus 로고    scopus 로고
    • Distinctive patterns of age-dependent hypomethylation in interspersed repetitive sequences
    • Jintaridth P, Mutirangura A. 2010. Distinctive patterns of age-dependent hypomethylation in interspersed repetitive sequences. Physiol Genomics 41: 194-200.
    • (2010) Physiol Genomics , vol.41 , pp. 194-200
    • Jintaridth, P.1    Mutirangura, A.2
  • 54
    • 84863986133 scopus 로고    scopus 로고
    • Functions of DNA methylation: Islands, start sites, gene bodies and beyond
    • Jones PA. 2012. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet 13: 484-492.
    • (2012) Nat Rev Genet , vol.13 , pp. 484-492
    • Jones, P.A.1
  • 55
    • 78049443508 scopus 로고    scopus 로고
    • Methods for DNA methylation analysis and applications in colon cancer
    • Jordà M, Peinado MA. 2010. Methods for DNA methylation analysis and applications in colon cancer. Mutat Res 693: 84-93.
    • (2010) Mutat Res , vol.693 , pp. 84-93
    • Jordà, M.1    Peinado, M.A.2
  • 56
    • 25444475765 scopus 로고    scopus 로고
    • Genetic disruption of cytosine DNA methyltransferase enzymes induces chromosomal instability in human cancer cells
    • Karpf AR, Matsui S. 2005. Genetic disruption of cytosine DNA methyltransferase enzymes induces chromosomal instability in human cancer cells. Cancer Res 65: 8635-8639.
    • (2005) Cancer Res , vol.65 , pp. 8635-8639
    • Karpf, A.R.1    Matsui, S.2
  • 58
    • 77951120000 scopus 로고    scopus 로고
    • Alternative splicing and evolution: Diversification, exon definition and function
    • Keren H, Lev-Maor G, Ast G. 2010. Alternative splicing and evolution: diversification, exon definition and function. Nat Rev Genet 11: 345-355.
    • (2010) Nat Rev Genet , vol.11 , pp. 345-355
    • Keren, H.1    Lev-Maor, G.2    Ast, G.3
  • 59
    • 84876996918 scopus 로고    scopus 로고
    • TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
    • Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. 2013. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14: R36.
    • (2013) Genome Biol , vol.14 , pp. R36
    • Kim, D.1    Pertea, G.2    Trapnell, C.3    Pimentel, H.4    Kelley, R.5    Salzberg, S.L.6
  • 61
    • 77249137168 scopus 로고    scopus 로고
    • Principles and challenges of genome-wide DNA methylation analysis
    • Laird PW. 2010. Principles and challenges of genome-wide DNA methylation analysis. Nat Rev Genet 11: 191-203.
    • (2010) Nat Rev Genet , vol.11 , pp. 191-203
    • Laird, P.W.1
  • 62
    • 84927704067 scopus 로고    scopus 로고
    • The role of DNA methylation in directing the functional organization of the cancer epigenome
    • Lay FD, Liu Y, Kelly TK, Witt H, Farnham PJ, Jones PA, Berman BP. 2015. The role of DNA methylation in directing the functional organization of the cancer epigenome. Genome Res 25: 467-477.
    • (2015) Genome Res , vol.25 , pp. 467-477
    • Lay, F.D.1    Liu, Y.2    Kelly, T.K.3    Witt, H.4    Farnham, P.J.5    Jones, P.A.6    Berman, B.P.7
  • 65
  • 66
    • 84928199128 scopus 로고    scopus 로고
    • Dynamic Alu methylation during normal development, aging, and tumorigenesis
    • Luo Y, Lu X, Xie H. 2014. Dynamic Alu methylation during normal development, aging, and tumorigenesis. Biomed Res Int 2014: 784706.
    • (2014) Biomed Res Int , vol.2014 , pp. 784706
    • Luo, Y.1    Lu, X.2    Xie, H.3
  • 67
    • 84962861406 scopus 로고    scopus 로고
    • A knowledgebase of the human Alu repetitive elements
    • Mallona I, Jordà M, Peinado MA. 2016. A knowledgebase of the human Alu repetitive elements. J Biomed Inform 60: 77-83.
    • (2016) J Biomed Inform , vol.60 , pp. 77-83
    • Mallona, I.1    Jordà, M.2    Peinado, M.A.3
  • 70
    • 80052937538 scopus 로고    scopus 로고
    • Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates
    • Molaro A, Hodges E, Fang F, Song Q, McCombie WR, Hannon GJ, Smith AD. 2011. Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates. Cell 146: 1029-1041.
    • (2011) Cell , vol.146 , pp. 1029-1041
    • Molaro, A.1    Hodges, E.2    Fang, F.3    Song, Q.4    McCombie, W.R.5    Hannon, G.J.6    Smith, A.D.7
  • 72
    • 84955695193 scopus 로고    scopus 로고
    • A-to-I editing of coding and non-coding RNAs by ADARs
    • Nishikura K. 2016. A-to-I editing of coding and non-coding RNAs by ADARs. Nat Rev Mol Cell Biol 17: 83-96.
    • (2016) Nat Rev Mol Cell Biol , vol.17 , pp. 83-96
    • Nishikura, K.1
  • 74
    • 3543105225 scopus 로고    scopus 로고
    • Circular binary segmentation for the analysis of array-based DNA copy number data
    • Olshen AB, Venkatraman ES, Lucito R, Wigler M. 2004. Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 5: 557-572.
    • (2004) Biostatistics , vol.5 , pp. 557-572
    • Olshen, A.B.1    Venkatraman, E.S.2    Lucito, R.3    Wigler, M.4
  • 75
    • 0029149552 scopus 로고
    • Fingerprinting of DNA and RNA by arbitrarily primed polymerase chain reaction: Applications in cancer research
    • Perucho M, Welsh J, Peinado MA, Ionov Y, McClelland M. 1995. Fingerprinting of DNA and RNA by arbitrarily primed polymerase chain reaction: applications in cancer research. Methods Enzymol 254: 275-290.
    • (1995) Methods Enzymol , vol.254 , pp. 275-290
    • Perucho, M.1    Welsh, J.2    Peinado, M.A.3    Ionov, Y.4    McClelland, M.5
  • 78
    • 78349263025 scopus 로고    scopus 로고
    • Sensitive measurement of unmethylated repeat DNA sequences by end-specific PCR
    • Rand KN, Molloy PL. 2010. Sensitive measurement of unmethylated repeat DNA sequences by end-specific PCR. Biotechniques 49: xiii-xvii.
    • (2010) Biotechniques , vol.49 , pp. xiii-xvii
    • Rand, K.N.1    Molloy, P.L.2
  • 85
    • 40049112866 scopus 로고    scopus 로고
    • Evolutionary rate heterogeneity of Alu repeats upstream of the APOA5 gene. Do they regulate APOA5 expression?
    • Ruiz-Narváez EA, Campos H. 2008. Evolutionary rate heterogeneity of Alu repeats upstream of the APOA5 gene: Do they regulate APOA5 expression? J Hum Genet 53: 247-253.
    • (2008) J Hum Genet , vol.53 , pp. 247-253
    • Ruiz-Narváez, E.A.1    Campos, H.2
  • 86
    • 77952994784 scopus 로고    scopus 로고
    • Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types
    • Ryba T, Hiratani I, Lu J, Itoh M, Kulik M, Zhang J, Schulz TC, Robins AJ, Dalton S, Gilbert DM. 2010. Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types. Genome Res 20: 761-770.
    • (2010) Genome Res , vol.20 , pp. 761-770
    • Ryba, T.1    Hiratani, I.2    Lu, J.3    Itoh, M.4    Kulik, M.5    Zhang, J.6    Schulz, T.C.7    Robins, A.J.8    Dalton, S.9    Gilbert, D.M.10
  • 88
    • 68149126345 scopus 로고    scopus 로고
    • Chromatin remodeling at Alu repeats by epigenetic treatment activates silenced microRNA-512-5p with downregulation of Mcl-1 in human gastric cancer cells
    • Saito Y, Suzuki H, Tsugawa H, Nakagawa I, Matsuzaki J, Kanai Y, Hibi T. 2009. Chromatin remodeling at Alu repeats by epigenetic treatment activates silenced microRNA-512-5p with downregulation of Mcl-1 in human gastric cancer cells. Oncogene 28: 2738-2744.
    • (2009) Oncogene , vol.28 , pp. 2738-2744
    • Saito, Y.1    Suzuki, H.2    Tsugawa, H.3    Nakagawa, I.4    Matsuzaki, J.5    Kanai, Y.6    Hibi, T.7
  • 89
    • 47849088254 scopus 로고    scopus 로고
    • Epigenetic nucleosomes: Alu sequences and CG as nucleosome positioning element
    • Salih F, Salih B, Kogan S, Trifonov EN. 2008. Epigenetic nucleosomes: Alu sequences and CG as nucleosome positioning element. J Biomol Struct Dyn 26: 9-16.
    • (2008) J Biomol Struct Dyn , vol.26 , pp. 9-16
    • Salih, F.1    Salih, B.2    Kogan, S.3    Trifonov, E.N.4
  • 91
    • 84922621952 scopus 로고    scopus 로고
    • Function and information content of DNA methylation
    • Schübeler D. 2015. Function and information content of DNA methylation. Nature 517: 321-326.
    • (2015) Nature , vol.517 , pp. 321-326
    • Schübeler, D.1
  • 92
    • 84865248380 scopus 로고    scopus 로고
    • Chromatin organization is a major influence on regional mutation rates in human cancer cells
    • Schuster-Böckler B, Lehner B. 2012. Chromatin organization is a major influence on regional mutation rates in human cancer cells. Nature 488: 504-507.
    • (2012) Nature , vol.488 , pp. 504-507
    • Schuster-Böckler, B.1    Lehner, B.2
  • 93
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • Smith TF, Waterman MS. 1981. Identification of common molecular subsequences. J Mol Biol 147: 195-197.
    • (1981) J Mol Biol , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 96
    • 43749098985 scopus 로고    scopus 로고
    • DNA methylation landscapes: Provocative insights from epigenomics
    • Suzuki MM, Bird A. 2008. DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet 9: 465-476.
    • (2008) Nat Rev Genet , vol.9 , pp. 465-476
    • Suzuki, M.M.1    Bird, A.2
  • 100
    • 83855165105 scopus 로고    scopus 로고
    • Repetitive DNA and next-generation sequencing: Computational challenges and solutions
    • Treangen TJ, Salzberg SL. 2012. Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat Rev Genet 13: 36-46.
    • (2012) Nat Rev Genet , vol.13 , pp. 36-46
    • Treangen, T.J.1    Salzberg, S.L.2
  • 101
    • 84925355722 scopus 로고    scopus 로고
    • SINE transcription by RNA polymerase III is suppressed by histone methylation but not by DNA methylation
    • Varshney D, Vavrova-Anderson J, Oler AJ, Cowling VH, Cairns BR, White RJ. 2015. SINE transcription by RNA polymerase III is suppressed by histone methylation but not by DNA methylation. Nat Commun 6: 6569.
    • (2015) Nat Commun , vol.6 , pp. 6569
    • Varshney, D.1    Vavrova-Anderson, J.2    Oler, A.J.3    Cowling, V.H.4    Cairns, B.R.5    White, R.J.6
  • 102
    • 34147104969 scopus 로고    scopus 로고
    • A faster circular binary segmentation algorithm for the analysis of array CGH data
    • Venkatraman ES, Olshen AB. 2007. A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics 23: 657-663.
    • (2007) Bioinformatics , vol.23 , pp. 657-663
    • Venkatraman, E.S.1    Olshen, A.B.2
  • 108
    • 77949437852 scopus 로고    scopus 로고
    • Methylation status of individual CpG sites within Alu elements in the human genome and Alu hypomethylation in gastric carcinomas
    • Xiang S, Liu Z, Zhang B, Zhou J, Zhu BD, Ji J, Deng D. 2010. Methylation status of individual CpG sites within Alu elements in the human genome and Alu hypomethylation in gastric carcinomas. BMC Cancer 10: 44.
    • (2010) BMC Cancer , vol.10 , pp. 44
    • Xiang, S.1    Liu, Z.2    Zhang, B.3    Zhou, J.4    Zhu, B.D.5    Ji, J.6    Deng, D.7
  • 111
    • 84879611157 scopus 로고    scopus 로고
    • DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape
    • Xie M, Hong C, Zhang B, Lowdon RF, Xing X, Li D, Zhou X, Lee HJ, Maire CL, Ligon KL, et al. 2013. DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape. Nat Genet 45: 836-841.
    • (2013) Nat Genet , vol.45 , pp. 836-841
    • Xie, M.1    Hong, C.2    Zhang, B.3    Lowdon, R.F.4    Xing, X.5    Li, D.6    Zhou, X.7    Lee, H.J.8    Maire, C.L.9    Ligon, K.L.10
  • 112
    • 2342557977 scopus 로고    scopus 로고
    • A simple method for estimating global DNA methylation using bisulfite PCR of repetitive DNA elements
    • Yang AS, Estecio MR, Doshi K, Kondo Y, Tajara EH, Issa JP. 2004. A simple method for estimating global DNA methylation using bisulfite PCR of repetitive DNA elements. Nucleic Acids Res 32: e38.
    • (2004) Nucleic Acids Res , vol.32 , pp. e38
    • Yang, A.S.1    Estecio, M.R.2    Doshi, K.3    Kondo, Y.4    Tajara, E.H.5    Issa, J.P.6


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