메뉴 건너뛰기




Volumn 122, Issue 25, 2013, Pages

Genome-wide methylation analyses of primary human leukocyte subsets identifies functionally important cell-type-specific hypomethylated regions

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

EID: 84891332899     PISSN: 00064971     EISSN: 15280020     Source Type: Journal    
DOI: 10.1182/blood-2013-05-503201     Document Type: Article
Times cited : (58)

References (39)
  • 1
    • 80052918929 scopus 로고    scopus 로고
    • Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment
    • Hodges E, Molaro A, Dos Santos CO, et al. Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment. Mol Cell. 2011;44(1): 17-28.
    • (2011) Mol Cell , vol.44 , Issue.1 , pp. 17-28
    • Hodges, E.1    Molaro, A.2    Dos Santos, C.O.3
  • 2
    • 66149147557 scopus 로고    scopus 로고
    • Developmental programming of CpG island methylation profiles in the human genome
    • Straussman R, Nejman D, Roberts D, et al. Developmental programming of CpG island methylation profiles in the human genome. Nat Struct Mol Biol. 2009;16(5): 564-571.
    • (2009) Nat Struct Mol Biol , vol.16 , Issue.5 , pp. 564-571
    • Straussman, R.1    Nejman, D.2    Roberts, D.3
  • 3
    • 79955583542 scopus 로고    scopus 로고
    • Mapping and analysis of chromatin state dynamics in nine human cell types
    • Ernst J, Kheradpour P, Mikkelsen TS, et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature. 2011; 473(7345): 43-49.
    • (2011) Nature , vol.473 , Issue.7345 , pp. 43-49
    • Ernst, J.1    Kheradpour, P.2    Mikkelsen, T.S.3
  • 4
    • 84863986133 scopus 로고    scopus 로고
    • Functions of DNA methylation: Islands, start sites, gene bodies and beyond
    • Jones PA. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet. 2012;13(7): 484-492.
    • (2012) Nat Rev Genet , vol.13 , Issue.7 , pp. 484-492
    • Jones, P.A.1
  • 5
    • 77249170184 scopus 로고    scopus 로고
    • Establishing, maintaining and modifying DNA methylation patterns in plants and animals
    • Law JA, Jacobsen SE. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet. 2010;11(3): 204-220.
    • (2010) Nat Rev Genet , vol.11 , Issue.3 , pp. 204-220
    • Law, J.A.1    Jacobsen, S.E.2
  • 6
    • 77957970301 scopus 로고    scopus 로고
    • Epigenetic modifications and human disease
    • Portela A, Esteller M. Epigenetic modifications and human disease. Nat Biotechnol. 2010;28(10): 1057-1068.
    • (2010) Nat Biotechnol , vol.28 , Issue.10 , pp. 1057-1068
    • Portela, A.1    Esteller, M.2
  • 7
    • 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. 2009;10(5): 295-304.
    • (2009) Nat Rev Genet , vol.10 , Issue.5 , pp. 295-304
    • Cedar, H.1    Bergman, Y.2
  • 8
    • 79959674418 scopus 로고    scopus 로고
    • Epigenetics of haematopoietic cell development
    • Cedar H, Bergman Y. Epigenetics of haematopoietic cell development. Nat Rev Immunol. 2011;11(7): 478-488.
    • (2011) Nat Rev Immunol , vol.11 , Issue.7 , pp. 478-488
    • Cedar, H.1    Bergman, Y.2
  • 9
    • 77954504873 scopus 로고    scopus 로고
    • Conserved role of intragenic DNA methylation in regulating alternative promoters
    • Maunakea AK, Nagarajan RP, Bilenky M, et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010; 466(7303): 253-257.
    • (2010) Nature , vol.466 , Issue.7303 , pp. 253-257
    • Maunakea, A.K.1    Nagarajan, R.P.2    Bilenky, M.3
  • 10
    • 84855956247 scopus 로고    scopus 로고
    • Epigenetics and the environment: Emerging patterns and implications
    • Feil R, Fraga MF. Epigenetics and the environment: emerging patterns and implications. Nat Rev Genet. 2011;13(2): 97-109.
    • (2011) Nat Rev Genet , vol.13 , Issue.2 , pp. 97-109
    • Feil, R.1    Fraga, M.F.2
  • 11
    • 79955623575 scopus 로고    scopus 로고
    • Epigenetic alterations in autoimmune rheumatic diseases
    • Ballestar E. Epigenetic alterations in autoimmune rheumatic diseases. Nat Rev Rheumatol. 2011; 7(5): 263-271.
    • (2011) Nat Rev Rheumatol , vol.7 , Issue.5 , pp. 263-271
    • Ballestar, E.1
  • 12
    • 79959872458 scopus 로고    scopus 로고
    • Cell typespecific DNA methylation at intragenic CpG islands in the immune system
    • Deaton AM, Webb S, Kerr AR, et al. Cell typespecific DNA methylation at intragenic CpG islands in the immune system. Genome Res. 2011;21(7): 1074-1086.
    • (2011) Genome Res , vol.21 , Issue.7 , pp. 1074-1086
    • Deaton, A.M.1    Webb, S.2    Kerr, A.R.3
  • 13
    • 84855292213 scopus 로고    scopus 로고
    • A promoter DNA demethylation landscape of human hematopoietic differentiation
    • Calvanese V, Fernández AF, Urdinguio RG, et al. A promoter DNA demethylation landscape of human hematopoietic differentiation. Nucleic Acids Res. 2012;40(1): 116-131.
    • (2012) Nucleic Acids Res , vol.40 , Issue.1 , pp. 116-131
    • Calvanese, V.1    Fernández, A.F.2    Urdinguio, R.G.3
  • 14
    • 79955970344 scopus 로고    scopus 로고
    • Genome-wide promoter DNA methylation dynamics of human hematopoietic progenitor cells during differentiation and aging
    • Bocker MT, Hellwig I, Breiling A, Eckstein V, Ho AD, Lyko F. Genome-wide promoter DNA methylation dynamics of human hematopoietic progenitor cells during differentiation and aging. Blood. 2011;117(19):e182-e189.
    • (2011) Blood , vol.117 , Issue.19
    • Bocker, M.T.1    Hellwig, I.2    Breiling, A.3    Eckstein, V.4    Ho, A.D.5    Lyko, F.6
  • 15
    • 80053304450 scopus 로고    scopus 로고
    • High density DNA methylation array with single CpG site resolution
    • Bibikova M, Barnes B, Tsan C, et al. High density DNA methylation array with single CpG site resolution. Genomics. 2011;98(4): 288-295.
    • (2011) Genomics , vol.98 , Issue.4 , pp. 288-295
    • Bibikova, M.1    Barnes, B.2    Tsan, C.3
  • 16
    • 77957937011 scopus 로고    scopus 로고
    • Quantitative comparison of genome-wide DNA methylation mapping technologies
    • Bock C, Tomazou EM, Brinkman AB, et al. Quantitative comparison of genome-wide DNA methylation mapping technologies. Nat Biotechnol. 2010;28(10): 1106-1114.
    • (2010) Nat Biotechnol , vol.28 , Issue.10 , pp. 1106-1114
    • Bock, C.1    Tomazou, E.M.2    Brinkman, A.B.3
  • 18
    • 33947410350 scopus 로고    scopus 로고
    • Microarray analysis of human leucocyte subsets: The advantages of positive selection and rapid purification
    • Lyons PA, Koukoulaki M, Hatton A, et al. Microarray analysis of human leucocyte subsets: the advantages of positive selection and rapid purification. BMC Genomics. 2007;8:64.
    • (2007) BMC Genomics , vol.8 , pp. 64
    • Lyons, P.A.1    Koukoulaki, M.2    Hatton, A.3
  • 19
    • 84870525593 scopus 로고    scopus 로고
    • A comparison of the whole genome approach of MeDIP-seq to the targeted approach of the Infinium HumanMethylation450 BeadChip(-) for methylome profiling
    • Clark C, Palta P, Joyce CJ, et al. A comparison of the whole genome approach of MeDIP-seq to the targeted approach of the Infinium HumanMethylation450 BeadChip(-) for methylome profiling. PLoS ONE. 2012;7(11): e50233.
    • (2012) PLoS ONE , vol.7 , Issue.11
    • Clark, C.1    Palta, P.2    Joyce, C.J.3
  • 20
    • 46249088370 scopus 로고    scopus 로고
    • Lumi: A pipeline for processing Illumina microarray
    • DOI 10.1093/bioinformatics/btn224
    • Du P, Kibbe WA, Lin SM. lumi: a pipeline for processing Illumina microarray. Bioinformatics. 2008;24(13): 1547-1548. (Pubitemid 351911712)
    • (2008) Bioinformatics , vol.24 , Issue.13 , pp. 1547-1548
    • Du, P.1    Kibbe, W.A.2    Lin, S.M.3
  • 21
    • 78649475003 scopus 로고    scopus 로고
    • Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis
    • Du P, Zhang X, Huang CC, et al. Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis. BMC Bioinformatics. 2010;11:587.
    • (2010) BMC Bioinformatics , vol.11 , pp. 587
    • Du, P.1    Zhang, X.2    Huang, C.C.3
  • 22
    • 4544341015 scopus 로고    scopus 로고
    • Linear models and empirical bayes methods for assessing differential expression in microarray experiments
    • Article 3
    • Smyth GK. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol. 2004;3:Article 3.
    • (2004) Stat Appl Genet Mol Biol , vol.3
    • Smyth, G.K.1
  • 23
    • 11244346557 scopus 로고    scopus 로고
    • Variance stabilization applied to microarray data calibration and to the quantification of differential expression
    • Huber W, von Heydebreck A, Sültmann H, Poustka A, Vingron M. Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics. 2002;18(suppl 1):S96-S104. (Pubitemid 41185642)
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. 1
    • Huber, W.1    Von Heydebreck, A.2    Sultmann, H.3    Poustka, A.4    Vingron, M.5
  • 24
    • 0142121516 scopus 로고    scopus 로고
    • Exploration, normalization, and summaries of high density oligonucleotide array probe level data
    • Irizarry RA, Hobbs B, Collin F, et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003;4(2): 249-264.
    • (2003) Biostatistics , vol.4 , Issue.2 , pp. 249-264
    • Irizarry, R.A.1    Hobbs, B.2    Collin, F.3
  • 25
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25(14): 1754-1760.
    • (2009) Bioinformatics , vol.25 , Issue.14 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 26
    • 77953718058 scopus 로고    scopus 로고
    • Novel expression signatures identified by transcriptional analysis of separated leucocyte subsets in systemic lupus erythematosus and vasculitis
    • Lyons PA, McKinney EF, Rayner TF, et al. Novel expression signatures identified by transcriptional analysis of separated leucocyte subsets in systemic lupus erythematosus and vasculitis. Ann Rheum Dis. 2010;69(6): 1208-1213.
    • (2010) Ann Rheum Dis , vol.69 , Issue.6 , pp. 1208-1213
    • Lyons, P.A.1    McKinney, E.F.2    Rayner, T.F.3
  • 27
    • 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, Park IH, Wen B, et al. Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts. Nat Genet. 2009;41(12): 1350-1353.
    • (2009) Nat Genet , vol.41 , Issue.12 , pp. 1350-1353
    • Doi, A.1    Park, I.H.2    Wen, B.3
  • 28
    • 77956902023 scopus 로고    scopus 로고
    • Comprehensive methylome map of lineage commitment from haematopoietic progenitors
    • Ji H, Ehrlich LI, Seita J, et al. Comprehensive methylome map of lineage commitment from haematopoietic progenitors. Nature. 2010; 467(7313): 338-342.
    • (2010) Nature , vol.467 , Issue.7313 , pp. 338-342
    • Ji, H.1    Ehrlich, L.I.2    Seita, J.3
  • 29
    • 59149084538 scopus 로고    scopus 로고
    • The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissuespecific CpG island shores
    • Irizarry RA, Ladd-Acosta C, Wen B, et al. The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissuespecific CpG island shores. Nat Genet. 2009; 41(2): 178-186.
    • (2009) Nat Genet , vol.41 , Issue.2 , pp. 178-186
    • Irizarry, R.A.1    Ladd-Acosta, C.2    Wen, B.3
  • 30
    • 77249137168 scopus 로고    scopus 로고
    • Principles and challenges of genomewide DNA methylation analysis
    • Laird PW. Principles and challenges of genomewide DNA methylation analysis. Nat Rev Genet. 2010;11(3): 191-203.
    • (2010) Nat Rev Genet , vol.11 , Issue.3 , pp. 191-203
    • Laird, P.W.1
  • 31
    • 67349120686 scopus 로고    scopus 로고
    • Genetic susceptibility to SLE: New insights from fine mapping and genome-wide association studies
    • Harley IT, Kaufman KM, Langefeld CD, Harley JB, Kelly JA. Genetic susceptibility to SLE: new insights from fine mapping and genome-wide association studies. Nat Rev Genet. 2009;10(5): 285-290.
    • (2009) Nat Rev Genet , vol.10 , Issue.5 , pp. 285-290
    • Harley, I.T.1    Kaufman, K.M.2    Langefeld, C.D.3    Harley, J.B.4    Kelly, J.A.5
  • 32
    • 44349124113 scopus 로고    scopus 로고
    • The genetics and immunopathogenesis of inflammatory bowel disease
    • DOI 10.1038/nri2340, PII NRI2340
    • Cho JH. The genetics and immunopathogenesis of inflammatory bowel disease. Nat Rev Immunol. 2008;8(6): 458-466. (Pubitemid 351733422)
    • (2008) Nature Reviews Immunology , vol.8 , Issue.6 , pp. 458-466
    • Cho, J.H.1
  • 33
    • 80054746235 scopus 로고    scopus 로고
    • Understanding type 1 diabetes through genetics: Advances and prospects
    • Polychronakos C, Li Q. Understanding type 1 diabetes through genetics: advances and prospects. Nat Rev Genet. 2011;12(11): 781-792.
    • (2011) Nat Rev Genet , vol.12 , Issue.11 , pp. 781-792
    • Polychronakos, C.1    Li, Q.2
  • 34
    • 78649489009 scopus 로고    scopus 로고
    • Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci
    • Franke A, McGovern DP, Barrett JC, et al. Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. Nat Genet. 2010;42(12): 1118-1125.
    • (2010) Nat Genet , vol.42 , Issue.12 , pp. 1118-1125
    • Franke, A.1    McGovern, D.P.2    Barrett, J.C.3
  • 35
    • 79952195585 scopus 로고    scopus 로고
    • Metaanalysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47
    • Anderson CA, Boucher G, Lees CW, et al. Metaanalysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47. Nat Genet. 2011;43(3): 246-252.
    • (2011) Nat Genet , vol.43 , Issue.3 , pp. 246-252
    • Anderson, C.A.1    Boucher, G.2    Lees, C.W.3
  • 36
    • 79953208931 scopus 로고    scopus 로고
    • Genome-wide association study identifies 12 new susceptibility loci for primary biliary cirrhosis
    • UK PBC Consortium; Wellcome Trust Case Control Consortium 3
    • Mells GF, Floyd JA, Morley KI, et al; UK PBC Consortium; Wellcome Trust Case Control Consortium 3. Genome-wide association study identifies 12 new susceptibility loci for primary biliary cirrhosis. Nat Genet. 2011; 43(4): 329-332.
    • (2011) Nat Genet , vol.43 , Issue.4 , pp. 329-332
    • Mells, G.F.1    Floyd, J.A.2    Morley, K.I.3
  • 37
    • 80054976037 scopus 로고    scopus 로고
    • Published correction appears
    • [published correction appears in Nat Genet. 2011;43(11): 1164].
    • (2011) Nat Genet , vol.43 , Issue.11 , pp. 1164
  • 38
    • 67349199566 scopus 로고    scopus 로고
    • Type 1 Diabetes Genetics Consortium. Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes
    • Barrett JC, Clayton DG, Concannon P, et al; Type 1 Diabetes Genetics Consortium. Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes. Nat Genet. 2009;41(6): 703-707.
    • (2009) Nat Genet , vol.41 , Issue.6 , pp. 703-707
    • Barrett, J.C.1    Clayton, D.G.2    Concannon, P.3
  • 39
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • and the ENCODE Project Consortium
    • Bernstein BE, Birney E, Dunham I et al, and the ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489(7414): 57-74.
    • (2012) Nature , vol.489 , Issue.7414 , pp. 57-74
    • Bernstein, B.E.1    Birney, E.2    Dunham, I.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.