메뉴 건너뛰기




Volumn 18, Issue 6, 2011, Pages 708-714

Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes

(24)  Martin, David a   Pantoja, Cristina b   Fernández Miñán, Ana c   Valdes Quezada, Christian d   Moltó, Eduardo e,f   Matesanz, Fuencisla g   Bogdanović, Ozren c   De La Calle Mustienes, Elisa c   Domínguez, Orlando b   Taher, Leila h   Furlan Magaril, Mayra d   Alcina, Antonio g   Cañóon, Susana i   Fedetz, María g   Blasco, María A b   Pereira, Paulo S j   Ovcharenko, Ivan h   Recillas Targa, Félix d   Montoliu, Lluís e,f   Manzanares, Miguel i   more..


Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR CTCF;

EID: 79958834622     PISSN: 15459993     EISSN: 15459985     Source Type: Journal    
DOI: 10.1038/nsmb.2059     Document Type: Article
Times cited : (74)

References (54)
  • 1
    • 45449096267 scopus 로고    scopus 로고
    • Tuning in to the signals: Noncoding sequence conservation in vertebrate genomes
    • Elgar, G. & Vavouri, T. Tuning in to the signals: noncoding sequence conservation in vertebrate genomes. Trends Genet. 24, 344-352 (2008).
    • (2008) Trends Genet. , vol.24 , pp. 344-352
    • Elgar, G.1    Vavouri, T.2
  • 2
    • 77954407332 scopus 로고    scopus 로고
    • Genomewide association studies and assessment of the risk of disease
    • Manolio, T.A. Genomewide association studies and assessment of the risk of disease. N. Engl. J. Med. 363, 166-176 (2010).
    • (2010) N. Engl. J. Med. , vol.363 , pp. 166-176
    • Manolio, T.A.1
  • 3
    • 70349623314 scopus 로고    scopus 로고
    • Cis-regulatory mutations in human disease
    • Epstein, D.J. Cis-regulatory mutations in human disease. Brief. Funct. Genomics Proteomics 8, 310-316 (2009).
    • (2009) Brief. Funct. Genomics Proteomics , vol.8 , pp. 310-316
    • Epstein, D.J.1
  • 4
    • 76249098866 scopus 로고    scopus 로고
    • Long-range gene regulation links genomic type 2 diabetes and obesity risk regions to HHEX, SOX4, and IRX3
    • Ragvin, A. et al. Long-range gene regulation links genomic type 2 diabetes and obesity risk regions to HHEX, SOX4, and IRX3. Proc. Natl. Acad. Sci. USA 107, 775-780 (2010).
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 775-780
    • Ragvin, A.1
  • 5
    • 67549119096 scopus 로고    scopus 로고
    • CTCF: Master weaver of the genome
    • Phillips, J.E. & Corces, V.G. CTCF: master weaver of the genome. Cell 137, 1194-1211 (2009).
    • (2009) Cell , vol.137 , pp. 1194-1211
    • Phillips, J.E.1    Corces, V.G.2
  • 7
    • 60149095014 scopus 로고    scopus 로고
    • Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains
    • Cuddapah, S. et al. Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains. Genome Res. 19, 24-32 (2009).
    • (2009) Genome Res. , vol.19 , pp. 24-32
    • Cuddapah, S.1
  • 8
    • 66149164708 scopus 로고    scopus 로고
    • Three subclasses of a Drosophila insulator show distinct and cell type-specific genomic distributions
    • Bushey, A.M., Ramos, E. & Corces, V.G. Three subclasses of a Drosophila insulator show distinct and cell type-specific genomic distributions. Genes Dev. 23, 1338-1350 (2009).
    • (2009) Genes Dev. , vol.23 , pp. 1338-1350
    • Bushey, A.M.1    Ramos, E.2    Corces, V.G.3
  • 9
    • 76749089660 scopus 로고    scopus 로고
    • A comprehensive map of insulator elements for the Drosophila genome
    • Nègre, N. et al. A comprehensive map of insulator elements for the Drosophila genome. PLoS Genet. 6, e1000814 (2010).
    • (2010) PLoS Genet. , vol.6
    • Nègre, N.1
  • 10
    • 77956189840 scopus 로고    scopus 로고
    • CTCF shapes chromatin by multiple mechanisms: The impact of 20 years of CTCF research on understanding the workings of chromatin
    • Ohlsson, R., Bartkuhn, M. & Renkawitz, R. CTCF shapes chromatin by multiple mechanisms: the impact of 20 years of CTCF research on understanding the workings of chromatin. Chromosoma 119, 351-360 (2010).
    • (2010) Chromosoma , vol.119 , pp. 351-360
    • Ohlsson, R.1    Bartkuhn, M.2    Renkawitz, R.3
  • 11
    • 33747885707 scopus 로고    scopus 로고
    • CTCF-dependent chromatin insulator is linked to epigenetic remodeling
    • DOI 10.1016/j.molcel.2006.08.008, PII S1097276506005673
    • Ishihara, K., Oshimura, M. & Nakao, M. CTCF-dependent chromatin insulator is linked to epigenetic remodeling. Mol. Cell 23, 733-742 (2006). (Pubitemid 44292561)
    • (2006) Molecular Cell , vol.23 , Issue.5 , pp. 733-742
    • Ishihara, K.1    Oshimura, M.2    Nakao, M.3
  • 12
    • 78349252731 scopus 로고    scopus 로고
    • Mediation of CTCF transcriptional insulation by DEAD-box RNA-binding protein p68 and steroid receptor RNA activator SRA
    • Yao, H. et al. Mediation of CTCF transcriptional insulation by DEAD-box RNA-binding protein p68 and steroid receptor RNA activator SRA. Genes Dev. 24, 2543-2555 (2010).
    • (2010) Genes Dev. , vol.24 , pp. 2543-2555
    • Yao, H.1
  • 13
    • 38849121606 scopus 로고    scopus 로고
    • Cohesins functionally associate with CTCF on mammalian chromosome arms
    • Parelho, V. et al. Cohesins functionally associate with CTCF on mammalian chromosome arms. Cell 132, 422-433 (2008).
    • (2008) Cell , vol.132 , pp. 422-433
    • Parelho, V.1
  • 16
    • 77957220857 scopus 로고    scopus 로고
    • Comparative epigenomic analysis of murine and human adipogenesis
    • Mikkelsen, T.S. et al. Comparative epigenomic analysis of murine and human adipogenesis. Cell 143, 156-169 (2010).
    • (2010) Cell , vol.143 , pp. 156-169
    • Mikkelsen, T.S.1
  • 17
    • 60149092301 scopus 로고    scopus 로고
    • Deep homology and the origins of evolutionary novelty
    • Shubin, N., Tabin, C. & Carroll, S. Deep homology and the origins of evolutionary novelty. Nature 457, 818-823 (2009).
    • (2009) Nature , vol.457 , pp. 818-823
    • Shubin, N.1    Tabin, C.2    Carroll, S.3
  • 18
    • 45549092100 scopus 로고    scopus 로고
    • The genetics of multiple sclerosis: SNPs to pathways to pathogenesis
    • DOI 10.1038/nrg2395, PII NRG2395
    • Oksenberg, J.R., Baranzini, S.E., Sawcer, S. & Hauser, S.L. The genetics of multiple sclerosis: SNPs to pathways to pathogenesis. Nat. Rev. Genet. 9, 516-526 (2008). (Pubitemid 351861542)
    • (2008) Nature Reviews Genetics , vol.9 , Issue.7 , pp. 516-526
    • Oksenberg, J.R.1    Baranzini, S.E.2    Sawcer, S.3    Hauser, S.L.4
  • 19
    • 77955812814 scopus 로고    scopus 로고
    • Genetic and environmental factors and the distribution of multiple sclerosis in Europe
    • Handel, A.E., Handunnetthi, L., Giovannoni, G., Ebers, G.C. & Ramagopalan, S.V. Genetic and environmental factors and the distribution of multiple sclerosis in Europe. Eur. J. Neurol. 17, 1210-1214 (2010).
    • (2010) Eur. J. Neurol. , vol.17 , pp. 1210-1214
    • Handel, A.E.1    Handunnetthi, L.2    Giovannoni, G.3    Ebers, G.C.4    Ramagopalan, S.V.5
  • 20
    • 77956061262 scopus 로고    scopus 로고
    • The genetics of multiple sclerosis: An update 2010
    • Hoffjan, S. & Akkad, D.A. The genetics of multiple sclerosis: an update 2010. Mol. Cell. Probes 24, 237-243 (2010).
    • (2010) Mol. Cell. Probes , vol.24 , pp. 237-243
    • Hoffjan, S.1    Akkad, D.A.2
  • 23
    • 67649881102 scopus 로고    scopus 로고
    • Genome-wide association study identifies new multiple sclerosis susceptibility loci on chromosomes 12 and 20
    • Australia and New Zealand Multiple Sclerosis Genetics Consortium (ANZgene)
    • Australia and New Zealand Multiple Sclerosis Genetics Consortium (ANZgene). Genome-wide association study identifies new multiple sclerosis susceptibility loci on chromosomes 12 and 20. Nat. Genet. 41, 824-828 (2009).
    • (2009) Nat. Genet. , vol.41 , pp. 824-828
  • 24
    • 77953808270 scopus 로고    scopus 로고
    • Tag-SNP analysis of the GFI1-EVI5-RPL5-FAM69 risk locus for multiple sclerosis
    • Alcina, A. et al. Tag-SNP analysis of the GFI1-EVI5-RPL5-FAM69 risk locus for multiple sclerosis. Eur. J. Hum. Genet. 18, 827-831 (2010).
    • (2010) Eur. J. Hum. Genet. , vol.18 , pp. 827-831
    • Alcina, A.1
  • 25
    • 52649132425 scopus 로고    scopus 로고
    • Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data
    • Jothi, R., Cuddapah, S., Barski, A., Cui, K. & Zhao, K. Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Res. 36, 5221-5231 (2008).
    • (2008) Nucleic Acids Res. , vol.36 , pp. 5221-5231
    • Jothi, R.1    Cuddapah, S.2    Barski, A.3    Cui, K.4    Zhao, K.5
  • 26
    • 75549089967 scopus 로고    scopus 로고
    • The UCSC Genome Browser database: Update 2010
    • Rhead, B. et al. The UCSC Genome Browser database: update 2010. Nucleic Acids Res. 38, D613-D619 (2010).
    • (2010) Nucleic Acids Res. , vol.38
    • Rhead, B.1
  • 27
    • 3242878193 scopus 로고    scopus 로고
    • ECR Browser: A tool for visualizing and accessing data from comparisons of multiple vertebrate genomes
    • DOI 10.1093/nar/gkh355
    • Ovcharenko, I., Nobrega, M.A., Loots, G.G. & Stubbs, L. ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes. Nucleic Acids Res. 32, W280-W286 (2004). (Pubitemid 38997344)
    • (2004) Nucleic Acids Research , vol.32 , Issue.WEB SERVER ISS.
    • Ovcharenko, I.1    Nobrega, M.A.2    Loots, G.G.3    Stubbs, L.4
  • 30
    • 0032530174 scopus 로고    scopus 로고
    • Loss of transcriptional activity of a transgene is accompanied by DNA methylation and histone deacetylation and is prevented by insulators
    • Pikaart, M.J., Recillas-Targa, F. & Felsenfeld, G. Loss of transcriptional activity of a transgene is accompanied by DNA methylation and histone deacetylation and is prevented by insulators. Genes Dev. 12, 2852-2862 (1998). (Pubitemid 28440144)
    • (1998) Genes and Development , vol.12 , Issue.18 , pp. 2852-2862
    • Pikaart, M.J.1    Recillas-Targa, F.2    Felsenfeld, G.3
  • 32
    • 35548990188 scopus 로고    scopus 로고
    • We gather together: Insulators and genome organization
    • DOI 10.1016/j.gde.2007.08.005, PII S0959437X07001566, Differentiation and Gene Regulation
    • Wallace, J.A. & Felsenfeld, G. We gather together: insulators and genome organization. Curr. Opin. Genet. Dev. 17, 400-407 (2007). (Pubitemid 350016897)
    • (2007) Current Opinion in Genetics and Development , vol.17 , Issue.5 , pp. 400-407
    • Wallace, J.A.1    Felsenfeld, G.2
  • 36
    • 70349085853 scopus 로고    scopus 로고
    • Zebrafish enhancer detection (ZED) vector: A new tool to facilitate transgenesis and the functional analysis of cis-regulatory regions in zebrafish
    • Bessa, J. et al. Zebrafish enhancer detection (ZED) vector: a new tool to facilitate transgenesis and the functional analysis of cis-regulatory regions in zebrafish. Dev. Dyn. 238, 2409-2417 (2009).
    • (2009) Dev. Dyn. , vol.238 , pp. 2409-2417
    • Bessa, J.1
  • 37
    • 77649299348 scopus 로고    scopus 로고
    • An atlas of combinatorial transcriptional regulation in mouse and man
    • Ravasi, T. et al. An atlas of combinatorial transcriptional regulation in mouse and man. Cell 140, 744-752 (2010).
    • (2010) Cell , vol.140 , pp. 744-752
    • Ravasi, T.1
  • 38
    • 11144339384 scopus 로고    scopus 로고
    • Long-range control of gene expression: Emerging mechanisms and disruption in disease
    • DOI 10.1086/426833
    • Kleinjan, D.A. & van Heyningen, V. Long-range control of gene expression: emerging mechanisms and disruption in disease. Am. J. Hum. Genet. 76, 8-32 (2005). (Pubitemid 40023762)
    • (2005) American Journal of Human Genetics , vol.76 , Issue.1 , pp. 8-32
    • Kleinjan, D.A.1    Van Heyningen, V.2
  • 39
    • 32944479751 scopus 로고    scopus 로고
    • Multiple sclerosis - A coordinated immune attack across the blood brain barrier
    • Hemmer, B., Cepok, S., Zhou, D. & Sommer, N. Multiple sclerosis - a coordinated immune attack across the blood brain barrier. Curr. Neurovasc. Res. 1, 141-150 (2004).
    • (2004) Curr. Neurovasc. Res. , vol.1 , pp. 141-150
    • Hemmer, B.1    Cepok, S.2    Zhou, D.3    Sommer, N.4
  • 40
    • 77954071946 scopus 로고    scopus 로고
    • Gfi1-cells and circuits: Unraveling transcriptional networks of development and disease
    • Phelan, J.D., Shroyer, N.F., Cook, T., Gebelein, B. & Grimes, H.L. Gfi1-cells and circuits: unraveling transcriptional networks of development and disease. Curr. Opin. Hematol. 17, 300-307 (2010).
    • (2010) Curr. Opin. Hematol. , vol.17 , pp. 300-307
    • Phelan, J.D.1    Shroyer, N.F.2    Cook, T.3    Gebelein, B.4    Grimes, H.L.5
  • 41
    • 77955298571 scopus 로고    scopus 로고
    • Gfi1 expression is controlled by five distinct regulatory regions spread over 100 kilobases, with Scl/Tal1, Gata2, PU.1, Erg, Meis1, and Runx1 acting as upstream regulators in early hematopoietic cells
    • Wilson, N.K. et al. Gfi1 expression is controlled by five distinct regulatory regions spread over 100 kilobases, with Scl/Tal1, Gata2, PU.1, Erg, Meis1, and Runx1 acting as upstream regulators in early hematopoietic cells. Mol. Cell. Biol. 30, 3853-3863 (2010).
    • (2010) Mol. Cell. Biol. , vol.30 , pp. 3853-3863
    • Wilson, N.K.1
  • 42
    • 77951203709 scopus 로고    scopus 로고
    • Microarray analysis identifies altered regulation of nuclear receptor family members in the pre-disease state of multiple sclerosis
    • Achiron, A. et al. Microarray analysis identifies altered regulation of nuclear receptor family members in the pre-disease state of multiple sclerosis. Neurobiol. Dis. 38, 201-209 (2010).
    • (2010) Neurobiol. Dis. , vol.38 , pp. 201-209
    • Achiron, A.1
  • 43
    • 33645460360 scopus 로고    scopus 로고
    • Oncogenic activity of Cdc6 through repression of the INK4/ARF locus
    • Gonzalez, S. et al. Oncogenic activity of Cdc6 through repression of the INK4/ARF locus. Nature 440, 702-706 (2006).
    • (2006) Nature , vol.440 , pp. 702-706
    • Gonzalez, S.1
  • 44
    • 37849044154 scopus 로고    scopus 로고
    • GATA-1 modulates the chromatin structure and activity of the chicken α-globin 3′ enhancer
    • Escamilla-Del-Arenal, M. & Recillas-Targa, F. GATA-1 modulates the chromatin structure and activity of the chicken α-globin 3′ enhancer. Mol. Cell. Biol. 28, 575-586 (2008).
    • (2008) Mol. Cell. Biol. , vol.28 , pp. 575-586
    • Escamilla-Del-Arenal, M.1    Recillas-Targa, F.2
  • 45
    • 70350170425 scopus 로고    scopus 로고
    • Chicken α-globin switching depends on autonomous silencing of the embryonic πglobin gene by epigenetics mechanisms
    • Rincón-Arano, H., Guerrero, G., Valdes-Quezada, C. & Recillas-Targa, F. Chicken α-globin switching depends on autonomous silencing of the embryonic πglobin gene by epigenetics mechanisms. J. Cell. Biochem. 108, 675-687 (2009).
    • (2009) J. Cell. Biochem. , vol.108 , pp. 675-687
    • Rincón-Arano, H.1    Guerrero, G.2    Valdes-Quezada, C.3    Recillas-Targa, F.4
  • 46
    • 75949108066 scopus 로고    scopus 로고
    • Galaxy: A web-based genome analysis tool for experimentalists
    • Blankenberg, D. et al. Galaxy: a web-based genome analysis tool for experimentalists. Curr. Protoc. Mol. Biol. 19, 19101-19121 (2010).
    • (2010) Curr. Protoc. Mol. Biol. , vol.19 , pp. 19101-19121
    • Blankenberg, D.1
  • 48
    • 67849114236 scopus 로고    scopus 로고
    • Pscan: Finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes
    • Zambelli, F., Pesole, G. & Pavesi, G. Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes. Nucleic Acids Res. 37, W247-W252 (2009).
    • (2009) Nucleic Acids Res. , vol.37
    • Zambelli, F.1    Pesole, G.2    Pavesi, G.3
  • 49
    • 33644876958 scopus 로고    scopus 로고
    • TRANSFAC and its module TRANSCompel: Transcriptional gene regulation in eukaryotes
    • Matys, V. et al. TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res. 34, D108-D110 (2006).
    • (2006) Nucleic Acids Res. , vol.34
    • Matys, V.1
  • 51
    • 20444365683 scopus 로고    scopus 로고
    • GOToolBox: Functional analysis of gene datasets based on Gene Ontology
    • Martin, D. et al. GOToolBox: functional analysis of gene datasets based on Gene Ontology. Genome Biol. 5, R101 (2004).
    • (2004) Genome Biol. , vol.5
    • Martin, D.1
  • 52
    • 33646133653 scopus 로고    scopus 로고
    • The UCSC known genes
    • Hsu, F. et al. The UCSC known genes. Bioinformatics 22, 1036-1046 (2006).
    • (2006) Bioinformatics , vol.22 , pp. 1036-1046
    • Hsu, F.1
  • 54
    • 0037083376 scopus 로고    scopus 로고
    • Capturing chromosome conformation
    • DOI 10.1126/science.1067799
    • Dekker, J., Rippe, K., Dekker, M. & Kleckner, N. Capturing chromosome conformation. Science 295, 1306-1311 (2002). (Pubitemid 34157624)
    • (2002) Science , vol.295 , Issue.5558 , pp. 1306-1311
    • Dekker, J.1    Rippe, K.2    Dekker, M.3    Kleckner, N.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.