Information de reference pour ce titreAccession Number: | 01217111-200806120-00017.
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Author: | Mrowka, Ralf 1,2,3; Bluthgen, Nils 4; Fahling, Michael 1,3
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Institution: | (1) Paul-Ehrlich-Zentrum fur Experimentelle Medizin, Berlin, Germany (2) AG Systems Biology - Computational Physiology, Berlin, Germany (3) Johannes-Muller-Institut fur Physiologie, Charite-Universitatsmedizin Berlin, Germany (4) School of Chemical Engineering and Analytical Sciences, Manchester Interdisciplinary Biocentre, University of Manchester, UK
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Source: | FEBS Journal. 275(12):3178-3192, June 2008.
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Abstract: | Reliable prediction of specific transcription factor target genes is a major challenge in systems biology and functional genomics. Current sequence-based methods yield many false predictions, due to the short and degenerated DNA-binding motifs. Here, we describe a new systematic genome-wide approach, the seed-distribution-distance method, that searches large-scale genome-wide expression data for genes that are similarly expressed as known targets. This method is used to identify genes that are likely targets, allowing sequence-based methods to focus on a subset of genes, giving rise to fewer false-positive predictions. We show by cross-validation that this method is robust in recovering specific target genes. Furthermore, this method identifies genes with typical functions and binding motifs of the seed. The method is illustrated by predicting novel targets of the transcription factor nuclear factor kappaB (NF-[kappa]B). Among the new targets is optineurin, which plays a key role in the pathogenesis of acquired blindness caused by adult-onset primary open-angle glaucoma. We show experimentally that the optineurin gene and other predicted genes are targets of NF-[kappa]B. Thus, our data provide a missing link in the signalling of NF-[kappa]B and the damping function of optineurin in signalling feedback of NF-[kappa]B. We present a robust and reliable method to enhance the genome-wide prediction of specific transcription factor target genes that exploits the vast amount of expression information available in public databases today.
Copyright (C) 2008 Blackwell Publishing Ltd.
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Author Keywords: | feedback; glaucoma; NF-[kappa]B; optineurin; transcription factor target prediction.
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References: | 1 Banerjee N & Zhang MQ (2002) Functional genomics as applied to mapping transcription regulatory networks. Curr Opin Microbiol 5, 313-317.
2 Cohen CD, Klingenhoff A, Boucherot A, Nitsche A, Henger A, Brunner B, Schmid H, Merkle M, Saleem MA, Koller KP et al. (2006) Comparative promoter analysis allows de novo identification of specialized cell junction-associated proteins. Proc Natl Acad Sci USA 103, 5682-5687.
3 Wingender E, Chen X, Fricke E, Geffers R, Hehl R, Liebich I, Krull M, Matys V, Michael H, Ohnhauser R et al. (2001) The TRANSFAC system on gene expression regulation. Nucleic Acids Res 29, 281-283.
4 Sandelin A, Alkema W, Engstrom P, Wasserman WW & Lenhard B (2004) JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res 32, D91-D94.
5 Wasserman WW & Sandelin A (2004) Applied bioinformatics for the identification of regulatory elements. Nat Rev Genet 5, 276-287.
6 Bulyk ML (2003) Computational prediction of transcription-factor binding site locations. Genome Biol 5, 201, doi: 10.1186/gb-2003-5-1-201.
7 Wasserman WW, Palumbo M, Thompson W, Fickett JW & Lawrence CE (2000) Human-mouse genome comparisons to locate regulatory sites. Nat Genet 26, 225-228.
8 Dieterich C, Grossmann S, Tanzer A, Ropcke S, Arndt PF, Stadler PF & Vingron M (2005) Comparative promoter region analysis powered by CORG. BMC Genomics 6, 24, doi: 10.1186/1471-2164-6-24.
9 Eisen MB, Spellman PT, Brown PO & Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95, 14863-14868.
10 Quackenbush J (2001) Computational analysis of microarray data. Nat Rev Genet 2, 418-427.
11 Beissbarth T (2006) Interpreting experimental results using gene ontologies. Methods Enzymol 411, 340-352.
12 Bluthgen N, Kielbasa SM & Herzel H (2005) Inferring combinatorial regulation of transcription in silico. Nucleic Acids Res 33, 272-279.
13 Qian Z, Lu L, Liu X, Cai YD & Li Y (2007) An approach to predict transcription factor DNA binding site specificity based upon gene and transcription factor functional categorization. Bioinformatics 23, 2449-2454.
14 Walker MG, Volkmuth W & Klingler TM (1999) Pharmaceutical target discovery using Guilt-by-Association: schizophrenia and Parkinson's disease genes. Proc Int Conf Intell Syst Mol Biol, 282-286.
15 Li A & Horvath S (2007) Network neighborhood analysis with the multi-node topological overlap measure. Bioinformatics 23, 222-231.
16 Tullai JW, Schaffer ME, Mullenbrock S, Kasif S & Cooper GM (2004) Identification of transcription factor binding sites upstream of human genes regulated by the phosphatidylinositol 3-kinase and MEK/ERK signaling pathways. J Biol Chem 279, 20167-20177.
17 Levenson JM, Choi S, Lee SY, Cao YA, Ahn HJ, Worley KC, Pizzi M, Liou HC & Sweatt JD (2004) A bioinformatics analysis of memory consolidation reveals involvement of the transcription factor c-rel. J Neurosci 24, 3933-3943.
18 Barenco M, Tomescu D, Brewer D, Callard R, Stark J & Hubank M (2006) Ranked prediction of p53 targets using hidden variable dynamic modeling. Genome Biol 7, R25.
19 Liu D, Umbach DM, Peddada SD, Li L, Crockett PW & Weinberg CR (2004) A random-periods model for expression of cell-cycle genes. Proc Natl Acad Sci USA 101, 7240-7245.
20 Brown PO & Botstein D (1999) Exploring the new world of the genome with DNA microarrays. Nat Genet 21, 33-37.
21 Dai X, He J & Zhao X (2007) A new systematic computational approach to predicting target genes of transcription factors. Nucleic Acids Res 35, 4433-4440.
22 Sarkar FH & Li Y (2008) NF-kappaB: a potential target for cancer chemoprevention and therapy. Front Biosci 13, 2950-2959.
23 Carmody RJ & Chen YH (2007) Nuclear factor-kappaB: activation and regulation during toll-like receptor signaling. Cell Mol Immunol 4, 31-41.
24 Hayden MS & Ghosh S (2004) Signaling to NF-kappaB. Genes Dev 18, 2195-2224.
25 Wu JT & Kral JG (2005) The NF-kappaB/IkappaB signaling system: a molecular target in breast cancer therapy. J Surg Res 123, 158-169.
26 Stuart JM, Segal E, Koller D & Kim SK (2003) A gene-coexpression network for global discovery of conserved genetic modules. Science 302, 249-255.
27 Demeter J, Beauheim C, Gollub J, Hernandez-Boussard T, Jin H, Maier D, Matese JC, Nitzberg M, Wymore F, Zachariah ZK et al. (2007) The Stanford Microarray Database: implementation of new analysis tools and open source release of software. Nucleic Acids Res 35, D766-D770.
28 Dieterich C, Cusack B, Wang H, Rateitschak K, Krause A & Vingron M (2002) Annotating regulatory DNA based on man-mouse genomic comparison. Bioinformatics 18(Suppl. 2), S84-S90.
29 Bracken AP, Ciro M, Cocito A & Helin K (2004) E2F target genes: unraveling the biology. Trends Biochem Sci 29, 409-417.
30 Xu X, Bieda M, Jin VX, Rabinovich A, Oberley MJ, Green R & Farnham PJ (2007) A comprehensive ChIP-chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members. Genome Res 17, 1550-1561.
31 Sementchenko VI & Watson DK (2000) Ets target genes: past, present and future. Oncogene 19, 6533-6548.
32 Hollenhorst PC, Shah AA, Hopkins C & Graves BJ (2007) Genome-wide analyses reveal properties of redundant and specific promoter occupancy within the ETS gene family. Genes Dev 21, 1882-1894.
33 Semenza GL (2003) Targeting HIF-1 for cancer therapy. Nat Rev Cancer 3, 721-732.
34 Fernandez PC, Frank SR, Wang L, Schroeder M, Liu S, Greene J, Cocito A & Amati B (2003) Genomic targets of the human c-Myc protein. Genes Dev 17, 1115-1129.
35 Wasserman WW & Fickett JW (1998) Identification of regulatory regions which confer muscle-specific gene expression. J Mol Biol 278, 167-181.
36 Yao Z, Cui Y, Watford WT, Bream JH, Yamaoka K, Hissong BD, Li D, Durum SK, Jiang Q, Bhandoola A et al. (2006) Stat5a/b are essential for normal lymphoid development and differentiation. Proc Natl Acad Sci USA 103, 1000-1005.
37 Moriggl R, Sexl V, Piekorz R, Topham D & Ihle JN (1999) Stat5 activation is uniquely associated with cytokine signaling in peripheral T cells. Immunity 11, 225-230.
38 Rezaie T, Child A, Hitchings R, Brice G, Miller L, Coca-Prados M, Heon E, Krupin T, Ritch R, Kreutzer D et al. (2002) Adult-onset primary open-angle glaucoma caused by mutations in optineurin. Science 295, 1077-1079.
39 Quigley HA (1996) Number of people with glaucoma worldwide. Br J Ophthalmol 80, 389-393.
40 Quigley HA & Vitale S (1997) Models of open-angle glaucoma prevalence and incidence in the United States. Invest Ophthalmol Vis Sci 38, 83-91.
41 Li Y, Kang J & Horwitz MS (1998) Interaction of an adenovirus E3 14.7-kilodalton protein with a novel tumor necrosis factor alpha-inducible cellular protein containing leucine zipper domains. Mol Cell Biol 18, 1601-1610.
42 De Marco N, Buono M, Troise F & Diez-Roux G (2006) Optineurin increases cell survival and translocates to the nucleus in a Rab8-dependent manner upon an apoptotic stimulus. J Biol Chem 281, 16147-16156.
43 Beg AA & Baltimore D (1996) An essential role for NF-kappaB in preventing TNF-alpha-induced cell death. Science 274, 782-784.
44 Zou JY & Crews FT (2005) TNF alpha potentiates glutamate neurotoxicity by inhibiting glutamate uptake in organotypic brain slice cultures: neuroprotection by NF kappa B inhibition. Brain Res 1034, 11-24.
45 Zhu G, Wu CJ, Zhao Y & Ashwell JD (2007) Optineurin negatively regulates TNFalpha-induced NF-kappaB activation by competing with NEMO for ubiquitinated RIP. Curr Biol 17, 1438-1443.
46 Rudolph D, Yeh WC, Wakeham A, Rudolph B, Nallainathan D, Potter J, Elia AJ & Mak TW (2000) Severe liver degeneration and lack of NF-kappaB activation in NEMO/IKKgamma-deficient mice. Genes Dev 14, 854-862.
47 David-Fung ES, Yui MA, Morales M, Wang H, Taghon T, Diamond RA & Rothenberg EV (2006) Progression of regulatory gene expression states in fetal and adult pro-T-cell development. Immunol Rev 209, 212-236.
48 Hitomi J, Katayama T, Eguchi Y, Kudo T, Taniguchi M, Koyama Y, Manabe T, Yamagishi S, Bando Y, Imaizumi K et al. (2004) Involvement of caspase-4 in endoplasmic reticulum stress-induced apoptosis and Abeta-induced cell death. J Cell Biol 165, 347-356.
49 Benos PV, Lapedes AS & Stormo GD (2002) Is there a code for protein-DNA recognition? Probab(ilistical)ly. Bioessays 24, 466-475.
50 Stormo GD (2000) DNA binding sites: representation and discovery. Bioinformatics 16, 16-23.
51 Roider HG, Kanhere A, Manke T & Vingron M (2007) Predicting transcription factor affinities to DNA from a biophysical model. Bioinformatics 23, 134-141.
52 Frith MC, Li MC & Weng Z (2003) Cluster-buster: finding dense clusters of motifs in DNA sequences. Nucleic Acids Res 31, 3666-3668.
53 Sandelin A, Carninci P, Lenhard B, Ponjavic J, Hayashizaki Y & Hume DA (2007) Mammalian RNA polymerase II core promoters: insights from genome-wide studies. Nat Rev Genet 8, 424-436.
54 Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T et al. (2002) The Ensembl genome database project. Nucleic Acids Res 30, 38-41.
55 Hammond MP & Birney E (2004) Genome information resources - developments at Ensembl. Trends Genet 20, 268-272.
56 Wingender E, Dietze P, Karas H & Knuppel R (1996) TRANSFAC: a database on transcription factors and their DNA binding sites. Nucleic Acids Res 24, 238-241.
57 Bluthgen N, Brand K, Cajavec B, Swat M, Herzel H & Beule D (2005) Biological profiling of gene groups utilizing gene ontology. Genome Inform Ser Workshop Genome Inform 16, 106-115.
58 Sun SC, Ganchi PA, Ballard DW & Greene WC (1993) NF-kappa B controls expression of inhibitor I kappaB alpha: evidence for an inducible autoregulatory pathway. Science 259, 1912-1915.
59 Edbrooke MR, Burt DW, Cheshire JK & Woo P (1989) Identification of cis-acting sequences responsible for phorbol ester induction of human serum amyloid A gene expression via a nuclear factor kappaB-like transcription factor. Mol Cell Biol 9, 1908-1916.
60 O'Donnell SM, Holm GH, Pierce JM, Tian B, Watson MJ, Chari RS, Ballard DW, Brasier AR & Dermody TS (2006) Identification of an NF-kappaB-dependent gene network in cells infected by mammalian reovirus. J Virol 80, 1077-1086.
61 Guitart A, Riezu-Boj JI, Elizalde E, Larrea E, Berasain C, Aldabe R, Civeira MP & Prieto J (2005) Hepatitis C virus infection of primary tupaia hepatocytes leads to selection of quasispecies variants, induction of interferon-stimulated genes and NF-kappaB nuclear translocation. J Gen Virol 86, 3065-3074.
62 Hosokawa Y, Suzuki H, Nakagawa M, Lee TH & Seto M (2005) API2-MALT1 fusion protein induces transcriptional activation of the API2 gene through NF-kappaB binding elements: evidence for a positive feed-back loop pathway resulting in unremitting NF-kappaB activation. Biochem Biophys Res Commun 334, 51-60.
63 Lombardi L, Ciana P, Cappellini C, Trecca D, Guerrini L, Migliazza A, Maiolo AT & Neri A (1995) Structural and functional characterization of the promoter regions of the NFKB2 gene. Nucleic Acids Res 23, 2328-2336.
64 Grall F, Gu X, Tan L, Cho JY, Inan MS, Pettit AR, Thamrongsak U, Choy BK, Manning C, Akbarali Y et al. (2003) Responses to the proinflammatory cytokines interleukin-1 and tumor necrosis factor alpha in cells derived from rheumatoid synovium and other joint tissues involve nuclear factor kappaB-mediated induction of the Ets transcription factor ESE-1. Arthritis Rheum 48, 1249-1260.
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Language: | English.
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Document Type: | Original Article.
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Journal Subset: | Life Sciences.
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ISSN: | 1742-464X
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NLM Journal Code: | 101229646
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