메뉴 건너뛰기




Volumn 12, Issue 7, 2011, Pages

Extensive characterization of NF-κB binding uncovers non-canonical motifs and advances the interpretation of genetic functional traits

Author keywords

[No Author keywords available]

Indexed keywords

IMMUNOGLOBULIN ENHANCER BINDING PROTEIN;

EID: 79960860669     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2011-12-7-r70     Document Type: Article
Times cited : (126)

References (52)
  • 2
    • 77954763156 scopus 로고    scopus 로고
    • Genome-wide allele-specific analysis: insights into regulatory variation.
    • Pastinen T. Genome-wide allele-specific analysis: insights into regulatory variation. Nat Rev Genet 2010, 11:533-538.
    • (2010) Nat Rev Genet , vol.11 , pp. 533-538
    • Pastinen, T.1
  • 3
    • 68949213578 scopus 로고    scopus 로고
    • Insights from genomic profiling of transcription factors.
    • 10.1038/nrg2636, 2846386, 19668247
    • Farnham PJ. Insights from genomic profiling of transcription factors. Nat Rev Genet 2009, 10:605-616. 10.1038/nrg2636, 2846386, 19668247.
    • (2009) Nat Rev Genet , vol.10 , pp. 605-616
    • Farnham, P.J.1
  • 4
    • 77951610155 scopus 로고    scopus 로고
    • Genetic analysis of variation in transcription factor binding in yeast.
    • 10.1038/nature08934, 2941147, 20237471
    • Zheng W, Zhao H, Mancera E, Steinmetz LM, Snyder M. Genetic analysis of variation in transcription factor binding in yeast. Nature 2010, 464:1187-1191. 10.1038/nature08934, 2941147, 20237471.
    • (2010) Nature , vol.464 , pp. 1187-1191
    • Zheng, W.1    Zhao, H.2    Mancera, E.3    Steinmetz, L.M.4    Snyder, M.5
  • 7
    • 70350731108 scopus 로고    scopus 로고
    • Distinguishing direct versus indirect transcription factor-DNA interactions.
    • 10.1101/gr.094144.109, 2775597, 19652015
    • Gordan R, Hartemink AJ, Bulyk ML. Distinguishing direct versus indirect transcription factor-DNA interactions. Genome Res 2009, 19:2090-2100. 10.1101/gr.094144.109, 2775597, 19652015.
    • (2009) Genome Res , vol.19 , pp. 2090-2100
    • Gordan, R.1    Hartemink, A.J.2    Bulyk, M.L.3
  • 11
    • 0033028741 scopus 로고    scopus 로고
    • Quantifying DNA-protein interactions by double-stranded DNA arrays.
    • 10.1038/9878, 10385322
    • Bulyk ML, Gentalen E, Lockhart DJ, Church GM. Quantifying DNA-protein interactions by double-stranded DNA arrays. Nat Biotechnol 1999, 17:573-577. 10.1038/9878, 10385322.
    • (1999) Nat Biotechnol , vol.17 , pp. 573-577
    • Bulyk, M.L.1    Gentalen, E.2    Lockhart, D.J.3    Church, G.M.4
  • 12
    • 0034651008 scopus 로고    scopus 로고
    • UPA, a universal protein array system for quantitative detection of protein-protein, protein-DNA, protein-RNA and protein-ligand interactions.
    • 10.1093/nar/28.2.e3, 102535, 10606671
    • Ge H. UPA, a universal protein array system for quantitative detection of protein-protein, protein-DNA, protein-RNA and protein-ligand interactions. Nucleic Acids Res 2000, 28:e3. 10.1093/nar/28.2.e3, 102535, 10606671.
    • (2000) Nucleic Acids Res , vol.28
    • Ge, H.1
  • 13
    • 2342507824 scopus 로고    scopus 로고
    • Quantitative high-throughput analysis of transcription factor binding specificities.
    • 10.1093/nar/gnh042, 390317, 14990752
    • Linnell J, Mott R, Field S, Kwiatkowski DP, Ragoussis J, Udalova IA. Quantitative high-throughput analysis of transcription factor binding specificities. Nucleic Acids Res 2004, 32:e44. 10.1093/nar/gnh042, 390317, 14990752.
    • (2004) Nucleic Acids Res , vol.32
    • Linnell, J.1    Mott, R.2    Field, S.3    Kwiatkowski, D.P.4    Ragoussis, J.5    Udalova, I.A.6
  • 14
    • 75649122221 scopus 로고    scopus 로고
    • Bind-n-Seq: high-throughput analysis of in vitro protein-DNA interactions using massively parallel sequencing.
    • 10.1093/nar/gkp802, 2794170, 19843614
    • Zykovich A, Korf I, Segal DJ. Bind-n-Seq: high-throughput analysis of in vitro protein-DNA interactions using massively parallel sequencing. Nucleic Acids Res 2009, 37:e151. 10.1093/nar/gkp802, 2794170, 19843614.
    • (2009) Nucleic Acids Res , vol.37
    • Zykovich, A.1    Korf, I.2    Segal, D.J.3
  • 15
    • 77958096076 scopus 로고    scopus 로고
    • Determining the specificity of protein-DNA interactions.
    • Stormo GD, Zhao Y. Determining the specificity of protein-DNA interactions. Nat Rev Genet 2010, 11:751-760.
    • (2010) Nat Rev Genet , vol.11 , pp. 751-760
    • Stormo, G.D.1    Zhao, Y.2
  • 16
    • 4544228457 scopus 로고    scopus 로고
    • Functions of NF-kappaB1 and NF-kappaB2 in immune cell biology.
    • 10.1042/BJ20040544, 1133795, 15214841
    • Beinke S, Ley SC. Functions of NF-kappaB1 and NF-kappaB2 in immune cell biology. Biochem J 2004, 382:393-409. 10.1042/BJ20040544, 1133795, 15214841.
    • (2004) Biochem J , vol.382 , pp. 393-409
    • Beinke, S.1    Ley, S.C.2
  • 17
    • 33750475618 scopus 로고    scopus 로고
    • Current insights into the regulation of programmed cell death by NF-kappaB.
    • 10.1038/sj.onc.1209938, 17072329
    • Dutta J, Fan Y, Gupta N, Fan G, Gelinas C. Current insights into the regulation of programmed cell death by NF-kappaB. Oncogene 2006, 25:6800-6816. 10.1038/sj.onc.1209938, 17072329.
    • (2006) Oncogene , vol.25 , pp. 6800-6816
    • Dutta, J.1    Fan, Y.2    Gupta, N.3    Fan, G.4    Gelinas, C.5
  • 18
    • 33750466230 scopus 로고    scopus 로고
    • Introduction to NF-kappaB: players, pathways, perspectives.
    • 10.1038/sj.onc.1209954, 17072321
    • Gilmore TD. Introduction to NF-kappaB: players, pathways, perspectives. Oncogene 2006, 25:6680-6684. 10.1038/sj.onc.1209954, 17072321.
    • (2006) Oncogene , vol.25 , pp. 6680-6684
    • Gilmore, T.D.1
  • 19
    • 33750435582 scopus 로고    scopus 로고
    • NF-kappaB and the immune response.
    • 10.1038/sj.onc.1209943, 17072327
    • Hayden MS, West AP, Ghosh S. NF-kappaB and the immune response. Oncogene 2006, 25:6758-6780. 10.1038/sj.onc.1209943, 17072327.
    • (2006) Oncogene , vol.25 , pp. 6758-6780
    • Hayden, M.S.1    West, A.P.2    Ghosh, S.3
  • 20
    • 0036781052 scopus 로고    scopus 로고
    • NF-kappaB regulation in the immune system.
    • 10.1038/nri910, 12360211
    • Li Q, Verma IM. NF-kappaB regulation in the immune system. Nat Rev Immunol 2002, 2:725-734. 10.1038/nri910, 12360211.
    • (2002) Nat Rev Immunol , vol.2 , pp. 725-734
    • Li, Q.1    Verma, I.M.2
  • 21
    • 0037062442 scopus 로고    scopus 로고
    • Quantitative prediction of NF-kappa B DNA-protein interactions.
    • 10.1073/pnas.102674699, 123039, 12048232
    • Udalova IA, Mott R, Field D, Kwiatkowski D. Quantitative prediction of NF-kappa B DNA-protein interactions. Proc Natl Acad Sci USA 2002, 99:8167-8172. 10.1073/pnas.102674699, 123039, 12048232.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 8167-8172
    • Udalova, I.A.1    Mott, R.2    Field, D.3    Kwiatkowski, D.4
  • 22
    • 0032992292 scopus 로고    scopus 로고
    • Construction, expression, purification and functional analysis of recombinant NFkappaB p50/p65 heterodimer.
    • 10.1093/protein/12.5.423, 10360983
    • Chen FE, Kempiak S, Huang DB, Phelps C, Ghosh G. Construction, expression, purification and functional analysis of recombinant NFkappaB p50/p65 heterodimer. Protein Eng 1999, 12:423-428. 10.1093/protein/12.5.423, 10360983.
    • (1999) Protein Eng , vol.12 , pp. 423-428
    • Chen, F.E.1    Kempiak, S.2    Huang, D.B.3    Phelps, C.4    Ghosh, G.5
  • 23
    • 0032556894 scopus 로고    scopus 로고
    • Crystal structure of p50/p65 heterodimer of transcription factor NF-kappaB bound to DNA.
    • 10.1038/34956, 9450761
    • Chen FE, Huang DB, Chen YQ, Ghosh G. Crystal structure of p50/p65 heterodimer of transcription factor NF-kappaB bound to DNA. Nature 1998, 391:410-413. 10.1038/34956, 9450761.
    • (1998) Nature , vol.391 , pp. 410-413
    • Chen, F.E.1    Huang, D.B.2    Chen, Y.Q.3    Ghosh, G.4
  • 25
    • 84870532154 scopus 로고    scopus 로고
    • Gene Expression Omnibus.
    • Gene Expression Omnibus. , http://www.ncbi.nlm.nih.gov/geo/
  • 26
    • 0036022523 scopus 로고    scopus 로고
    • High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites.
    • Roulet E, Busso S, Camargo AA, Simpson AJ, Mermod N, Bucher P. High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites. Nat Biotechnol 2002, 20:831-835.
    • (2002) Nat Biotechnol , vol.20 , pp. 831-835
    • Roulet, E.1    Busso, S.2    Camargo, A.A.3    Simpson, A.J.4    Mermod, N.5    Bucher, P.6
  • 27
    • 67249117049 scopus 로고    scopus 로고
    • Potential etiologic and functional implications of genome-wide association loci for human diseases and traits.
    • 10.1073/pnas.0903103106, 2687147, 19474294
    • Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, Manolio TA. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci USA 2009, 106:9362-9367. 10.1073/pnas.0903103106, 2687147, 19474294.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 9362-9367
    • Hindorff, L.A.1    Sethupathy, P.2    Junkins, H.A.3    Ramos, E.M.4    Mehta, J.P.5    Collins, F.S.6    Manolio, T.A.7
  • 28
    • 0034459681 scopus 로고    scopus 로고
    • Functional consequences of a polymorphism affecting NF-kappaB p50-p50 binding to the TNF promoter region.
    • 10.1128/MCB.20.24.9113-9119.2000, 102169, 11094063
    • Udalova IA, Richardson A, Denys A, Smith C, Ackerman H, Foxwell B, Kwiatkowski D. Functional consequences of a polymorphism affecting NF-kappaB p50-p50 binding to the TNF promoter region. Mol Cell Biol 2000, 20:9113-9119. 10.1128/MCB.20.24.9113-9119.2000, 102169, 11094063.
    • (2000) Mol Cell Biol , vol.20 , pp. 9113-9119
    • Udalova, I.A.1    Richardson, A.2    Denys, A.3    Smith, C.4    Ackerman, H.5    Foxwell, B.6    Kwiatkowski, D.7
  • 29
    • 0032993434 scopus 로고    scopus 로고
    • A polymorphism that affects OCT-1 binding to the TNF promoter region is associated with severe malaria.
    • 10.1038/9649, 10369255
    • Knight JC, Udalova I, Hill AV, Greenwood BM, Peshu N, Marsh K, Kwiatkowski D. A polymorphism that affects OCT-1 binding to the TNF promoter region is associated with severe malaria. Nat Genet 1999, 22:145-150. 10.1038/9649, 10369255.
    • (1999) Nat Genet , vol.22 , pp. 145-150
    • Knight, J.C.1    Udalova, I.2    Hill, A.V.3    Greenwood, B.M.4    Peshu, N.5    Marsh, K.6    Kwiatkowski, D.7
  • 30
    • 0031964687 scopus 로고    scopus 로고
    • A novel DNA recognition mode by the NF-kappa B p65 homodimer.
    • 10.1038/nsb0198-67, 9437432
    • Chen YQ, Ghosh S, Ghosh G. A novel DNA recognition mode by the NF-kappa B p65 homodimer. Nat Struct Biol 1998, 5:67-73. 10.1038/nsb0198-67, 9437432.
    • (1998) Nat Struct Biol , vol.5 , pp. 67-73
    • Chen, Y.Q.1    Ghosh, S.2    Ghosh, G.3
  • 31
    • 0034654832 scopus 로고    scopus 로고
    • NF-kappaB p65 (RelA) homodimer uses distinct mechanisms to recognize DNA targets.
    • 10.1016/S0969-2126(00)00123-4, 10801482
    • Chen YQ, Sengchanthalangsy LL, Hackett A, Ghosh G. NF-kappaB p65 (RelA) homodimer uses distinct mechanisms to recognize DNA targets. Structure 2000, 8:419-428. 10.1016/S0969-2126(00)00123-4, 10801482.
    • (2000) Structure , vol.8 , pp. 419-428
    • Chen, Y.Q.1    Sengchanthalangsy, L.L.2    Hackett, A.3    Ghosh, G.4
  • 32
    • 36549083316 scopus 로고    scopus 로고
    • In vitro selection of optimal RelB/p52 DNA-binding motifs.
    • 10.1016/j.bbrc.2007.10.200, 17996728
    • Britanova LV, Makeev VJ, Kuprash DV. In vitro selection of optimal RelB/p52 DNA-binding motifs. Biochem Biophys Res Commun 2008, 365:583-588. 10.1016/j.bbrc.2007.10.200, 17996728.
    • (2008) Biochem Biophys Res Commun , vol.365 , pp. 583-588
    • Britanova, L.V.1    Makeev, V.J.2    Kuprash, D.V.3
  • 33
    • 9144275033 scopus 로고    scopus 로고
    • Activation of IKKalpha target genes depends on recognition of specific kappaB binding sites by RelB:p52 dimers.
    • 10.1038/sj.emboj.7600391, 524385, 15470505
    • Bonizzi G, Bebien M, Otero DC, Johnson-Vroom KE, Cao Y, Vu D, Jegga AG, Aronow BJ, Ghosh G, Rickert RC, Karin M. Activation of IKKalpha target genes depends on recognition of specific kappaB binding sites by RelB:p52 dimers. EMBO J 2004, 23:4202-4210. 10.1038/sj.emboj.7600391, 524385, 15470505.
    • (2004) EMBO J , vol.23 , pp. 4202-4210
    • Bonizzi, G.1    Bebien, M.2    Otero, D.C.3    Johnson-Vroom, K.E.4    Cao, Y.5    Vu, D.6    Jegga, A.G.7    Aronow, B.J.8    Ghosh, G.9    Rickert, R.C.10    Karin, M.11
  • 34
    • 0034636161 scopus 로고    scopus 로고
    • Characterization of the DNA-binding domains from the yeast cell-cycle transcription factors Mbp1 and Swi4.
    • 10.1021/bi992212i, 10747782
    • Taylor IA, McIntosh PB, Pala P, Treiber MK, Howell S, Lane AN, Smerdon SJ. Characterization of the DNA-binding domains from the yeast cell-cycle transcription factors Mbp1 and Swi4. Biochemistry 2000, 39:3943-3954. 10.1021/bi992212i, 10747782.
    • (2000) Biochemistry , vol.39 , pp. 3943-3954
    • Taylor, I.A.1    McIntosh, P.B.2    Pala, P.3    Treiber, M.K.4    Howell, S.5    Lane, A.N.6    Smerdon, S.J.7
  • 35
    • 33745432883 scopus 로고    scopus 로고
    • Regulation of mating and filamentation genes by two distinct Ste12 complexes in Saccharomyces cerevisiae.
    • 10.1128/MCB.02053-05, 1489142, 16782869
    • Chou S, Lane S, Liu H. Regulation of mating and filamentation genes by two distinct Ste12 complexes in Saccharomyces cerevisiae. Mol Cell Biol 2006, 26:4794-4805. 10.1128/MCB.02053-05, 1489142, 16782869.
    • (2006) Mol Cell Biol , vol.26 , pp. 4794-4805
    • Chou, S.1    Lane, S.2    Liu, H.3
  • 36
    • 77956755980 scopus 로고    scopus 로고
    • Inflammatory bowel diseases, celiac disease, and bone.
    • 10.1016/j.abb.2010.06.026, 20599670
    • Bianchi ML. Inflammatory bowel diseases, celiac disease, and bone. Arch Biochem Biophys 2010, 503:54-65. 10.1016/j.abb.2010.06.026, 20599670.
    • (2010) Arch Biochem Biophys , vol.503 , pp. 54-65
    • Bianchi, M.L.1
  • 37
    • 77953555514 scopus 로고    scopus 로고
    • Cytokines as therapeutic targets in SLE.
    • 10.1038/nrrheum.2010.64, 20440285
    • Ronnblom L, Elkon KB. Cytokines as therapeutic targets in SLE. Nat Rev Rheumatol 2010, 6:339-347. 10.1038/nrrheum.2010.64, 20440285.
    • (2010) Nat Rev Rheumatol , vol.6 , pp. 339-347
    • Ronnblom, L.1    Elkon, K.B.2
  • 38
    • 77953749477 scopus 로고    scopus 로고
    • Biliary innate immunity in the pathogenesis of biliary diseases.
    • Harada K, Nakanuma Y. Biliary innate immunity in the pathogenesis of biliary diseases. Inflamm Allergy Drug Targets 2010, 9:83-90.
    • (2010) Inflamm Allergy Drug Targets , vol.9 , pp. 83-90
    • Harada, K.1    Nakanuma, Y.2
  • 39
    • 77957196913 scopus 로고    scopus 로고
    • Rheumatoid arthritis.
    • 10.1016/S0140-6736(10)60826-4, 20870100
    • Scott DL, Wolfe F, Huizinga TW. Rheumatoid arthritis. Lancet 2010, 376:1094-1108. 10.1016/S0140-6736(10)60826-4, 20870100.
    • (2010) Lancet , vol.376 , pp. 1094-1108
    • Scott, D.L.1    Wolfe, F.2    Huizinga, T.W.3
  • 40
    • 73949090103 scopus 로고    scopus 로고
    • Inflammation in neurodegenerative diseases.
    • 10.1111/j.1365-2567.2009.03225.x, 2814458, 20561356
    • Amor S, Puentes F, Baker D, van der Valk P. Inflammation in neurodegenerative diseases. Immunology 2010, 129:154-169. 10.1111/j.1365-2567.2009.03225.x, 2814458, 20561356.
    • (2010) Immunology , vol.129 , pp. 154-169
    • Amor, S.1    Puentes, F.2    Baker, D.3    van der Valk, P.4
  • 41
    • 33646066801 scopus 로고    scopus 로고
    • Molecular basis of common variable immunodeficiency.
    • 10.1016/j.jaci.2006.01.038, 16630927
    • Castigli E, Geha RS. Molecular basis of common variable immunodeficiency. J Allergy Clin Immunol 2006, 117:740-746; quiz 747. 10.1016/j.jaci.2006.01.038, 16630927.
    • (2006) J Allergy Clin Immunol , vol.117
    • Castigli, E.1    Geha, R.S.2
  • 42
    • 34047123640 scopus 로고    scopus 로고
    • Accuracy and reproducibility of protein-DNA microarray technology.
    • Field S, Udalova I, Ragoussis J. Accuracy and reproducibility of protein-DNA microarray technology. Adv Biochem Eng Biotechnol 2007, 104:87-110.
    • (2007) Adv Biochem Eng Biotechnol , vol.104 , pp. 87-110
    • Field, S.1    Udalova, I.2    Ragoussis, J.3
  • 43
    • 80053270072 scopus 로고    scopus 로고
    • Agilent Technologies eArray.
    • Agilent Technologies eArray. , https://earray.chem.agilent.com/earray/
  • 44
    • 59949083631 scopus 로고    scopus 로고
    • Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors.
    • 10.1038/nprot.2008.195, 2908410, 19265799
    • Berger MF, Bulyk ML. Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors. Nat Protoc 2009, 4:393-411. 10.1038/nprot.2008.195, 2908410, 19265799.
    • (2009) Nat Protoc , vol.4 , pp. 393-411
    • Berger, M.F.1    Bulyk, M.L.2
  • 45
    • 23644431878 scopus 로고    scopus 로고
    • In vitro selection of DNA binding sites for ABF1 protein from Saccharomyces cerevisiae.
    • 10.1016/j.febslet.2005.07.009, 16083878
    • Beinoraviciute-Kellner R, Lipps G, Krauss G. In vitro selection of DNA binding sites for ABF1 protein from Saccharomyces cerevisiae. FEBS Lett 2005, 579:4535-4540. 10.1016/j.febslet.2005.07.009, 16083878.
    • (2005) FEBS Lett , vol.579 , pp. 4535-4540
    • Beinoraviciute-Kellner, R.1    Lipps, G.2    Krauss, G.3
  • 47
    • 0041853625 scopus 로고    scopus 로고
    • MATCH: A tool for searching transcription factor binding sites in DNA sequences.
    • 10.1093/nar/gkg585, 169193, 12824369
    • Kel AE, Gossling E, Reuter I, Cheremushkin E, Kel-Margoulis OV, Wingender E. MATCH: A tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res 2003, 31:3576-3579. 10.1093/nar/gkg585, 169193, 12824369.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3576-3579
    • Kel, A.E.1    Gossling, E.2    Reuter, I.3    Cheremushkin, E.4    Kel-Margoulis, O.V.5    Wingender, E.6
  • 48
    • 84872976442 scopus 로고    scopus 로고
    • 1000 Genomes Project.
    • 1000 Genomes Project. , http://www.1000genomes.org/
  • 50
    • 84870445213 scopus 로고    scopus 로고
    • International HapMap Project.
    • International HapMap Project. , http://hapmap.ncbi.nlm.nih.gov/
  • 51
    • 32144452542 scopus 로고    scopus 로고
    • Sequence features of DNA binding sites reveal structural class of associated transcription factor.
    • 10.1093/bioinformatics/bti731, 16267080
    • Narlikar L, Hartemink AJ. Sequence features of DNA binding sites reveal structural class of associated transcription factor. Bioinformatics 2006, 22:157-163. 10.1093/bioinformatics/bti731, 16267080.
    • (2006) Bioinformatics , vol.22 , pp. 157-163
    • Narlikar, L.1    Hartemink, A.J.2
  • 52
    • 22344457014 scopus 로고    scopus 로고
    • EnoLOGOS: a versatile web tool for energy normalized sequence logos.
    • 10.1093/nar/gki439, 1160200, 15980495
    • Workman CT, Yin Y, Corcoran DL, Ideker T, Stormo GD, Benos PV. enoLOGOS: a versatile web tool for energy normalized sequence logos. Nucleic Acids Res 2005, 33:W389-392. 10.1093/nar/gki439, 1160200, 15980495.
    • (2005) Nucleic Acids Res , vol.33
    • Workman, C.T.1    Yin, Y.2    Corcoran, D.L.3    Ideker, T.4    Stormo, G.D.5    Benos, P.V.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.