PPARγ and NF-κB regulate the gene promoter activity of their shared repressor, TNIP1

Biochimica et Biophysica Acta - Gene Regulatory Mechanisms

Volumn 1819, Issue 1, 2012, Pages 1-15

  Gurevich, Igor ^a   Zhang, Carmen ^a   Encarnacao, Priscilla C ^a   Struzynski, Charles P ^a   Livings, Sarah E ^a   Aneskievich, Brian J ^a  

^a UNIVERSITY OF CONNECTICUT   (United States)

Author keywords

NF B; PPAR; Promoter; Response element; Transcriptional regulation

Indexed keywords

IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; PEROXISOME PROLIFERATOR; PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA; TNFAIP3 INTERACTING PROTEIN 1; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

ARTICLE; CELL FUNCTION; CHROMATIN IMMUNOPRECIPITATION; COMPUTER MODEL; CONTROLLED STUDY; ELECTROPHORESIS; ENZYME REGULATION; GENE EXPRESSION; HUMAN; HUMAN CELL; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN EXPRESSION; SIGNAL TRANSDUCTION; TATA BOX; TRANSCRIPTION REGULATION;

BASE SEQUENCE; BINDING SITES; DNA-BINDING PROTEINS; GENE EXPRESSION REGULATION; HELA CELLS; HUMANS; MOLECULAR SEQUENCE DATA; NF-KAPPA B; PEROXISOME PROLIFERATOR-ACTIVATED RECEPTORS; PPAR GAMMA; PROMOTER REGIONS, GENETIC; PROTEIN BINDING; REGULATORY SEQUENCES, NUCLEIC ACID; RESPONSE ELEMENTS; SIGNAL TRANSDUCTION; TRANSCRIPTION FACTOR RELA; TRANSCRIPTION INITIATION SITE; TRANSCRIPTIONAL ACTIVATION;

EID: 80755169304     PISSN: 18749399     EISSN: 18764320     Source Type: Journal    
DOI: 10.1016/j.bbagrm.2011.09.006     Document Type: Article

References (78)

1. Hosgood H.D., Menashe I., Shen M., Yeager M., Yuenger J., Rajaraman P., He X., Chatterjee N., Caporaso N.E., Zhu Y., Chanock S.J., Zheng T., Lan Q. Pathway-based evaluation of 380 candidate genes and lung cancer susceptibility suggests the importance of the cell cycle pathway. Carcinogenesis 2008, 29:1938-1943.
2. Nair R.P., Duffin K.C., Helms C., Ding J., Stuart P.E., Goldgar D., Gudjonsson J.E., Li Y., Tejasvi T., Feng B.J., Ruether A., Schreiber S., Weichenthal M., Gladman D., Rahman P., Schrodi S.J., Prahalad S., Guthery S.L., Fischer J., Liao W., Kwok P.Y., Menter A., Lathrop G.M., Wise C.A., Begovich A.B., Voorhees J.J., Elder J.T., Krueger G.G., Bowcock A.M., Abecasis G.R. Genome-wide scan reveals association of psoriasis with IL-23 and NF-kappaB pathways. Nat. Genet. 2009, 41:199-204.
3. Fukushi M., Dixon J., Kimura T., Tsurutani N., Dixon M.J., Yamamoto N. Identification and cloning of a novel cellular protein Naf1, Nef-associated factor 1, that increases cell surface CD4 expression. FEBS Lett. 1999, 442:83-88.
4. Gupta K., Ott D., Hope T.J., Siliciano R.F., Boeke J.D. A human nuclear shuttling protein that interacts with human immunodeficiency virus type 1 matrix is packaged into virions. J. Virol. 2000, 74:11811-11824.
5. Heyninck K., Kreike M.M., Beyaert R. Structure-function analysis of the A20-binding inhibitor of NF-kappa B activation, ABIN-1. FEBS Lett. 2003, 536:135-140.
6. Heyninck K., De Valck D., Vanden Berghe W., Van Criekinge W., Contreras R., Fiers W., Haegeman G., Beyaert R. The zinc finger protein A20 inhibits TNF-induced NF-kappaB-dependent gene expression by interfering with an RIP- or TRAF2-mediated transactivation signal and directly binds to a novel NF-kappaB-inhibiting protein ABIN. J. Cell Biol. 1999, 145:1471-1482.
7. Beyaert R., Heyninck K., Van Huffel S. A20 and A20-binding proteins as cellular inhibitors of nuclear factor-kappa B-dependent gene expression and apoptosis. Biochem. Pharmacol. 2000, 60:1143-1151.
8. Mauro C., Pacifico F., Lavorgna A., Mellone S., Iannetti A., Acquaviva R., Formisano S., Vito P., Leonardi A. ABIN-1 binds to NEMO/IKKgamma and co-operates with A20 in inhibiting NF-kappaB. J. Biol. Chem. 2006, 281:18482-18488.
9. Wagner S., Carpentier I., Rogov V., Kreike M., Ikeda F., Lohr F., Wu C.J., Ashwell J.D., Dotsch V., Dikic I., Beyaert R. Ubiquitin binding mediates the NF-kappaB inhibitory potential of ABIN proteins. Oncogene 2008, 27:3739-3745.
10. Oshima S., Turer E.E., Callahan J.A., Chai S., Advincula R., Barrera J., Shifrin N., Lee B., Yen B., Woo T., Malynn B.A., Ma A. ABIN-1 is a ubiquitin sensor that restricts cell death and sustains embryonic development. Nature 2009, 457:906-909.
11. Tian B., Nowak D.E., Jamaluddin M., Wang S., Brasier A.R. Identification of direct genomic targets downstream of the nuclear factor-kappaB transcription factor mediating tumor necrosis factor signaling. J. Biol. Chem. 2005, 280:17435-17448.
12. Gurevich I., Aneskievich B.J. Liganded RARalpha and RARgamma interact with but are repressed by TNIP1. Biochem. Biophys. Res. Commun. 2009, 389:409-414.
13. Gurevich I., Flores A.M., Aneskievich B.J. Corepressors of agonist-bound nuclear receptors. Toxicol. Appl. Pharmacol. 2007, 223:288-298.
14. Lonard D.M., Lanz R.B., O'Malley B.W. Nuclear receptor coregulators and human disease. Endocr. Rev. 2007, 28:575-587.
15. Augereau P., Badia E., Balaguer P., Carascossa S., Castet A., Jalaguier S., Cavailles V. Negative regulation of hormone signaling by RIP140. J. Steroid Biochem. Mol. Biol. 2006, 102:51-59.
16. White K.A., Yore M.M., Warburton S.L., Vaseva A.V., Rieder E., Freemantle S.J., Spinella M.J. Negative feedback at the level of nuclear receptor coregulation. J. Biol. Chem. 2003, 278:43889-43892.
17. Shiote Y., Ouchida M., Jitsumori Y., Ogama Y., Matsuo Y., Ishimaru F., Tanimoto M., Shimizu K. Multiple splicing variants of Naf1/ABIN-1 transcripts and their alterations in hematopoietic tumors. Int. J. Mol. Med. 2006, 18:917-923.
18. Cartharius K., Frech K., Grote K., Klocke B., Haltmeier M., Klingenhoff A., Frisch M., Bayerlein M., Werner T. MatInspector and beyond: promoter analysis based on transcription factor binding sites. Bioinformatics 2005, 21:2933-2942.
19. Matys V., Kel-Margoulis O.V., Fricke E., Liebich I., Land S., Barre-Dirrie A., Reuter I., Chekmenev D., Krull M., Hornischer K., Voss N., Stegmaier P., Lewicki-Potapov B., Saxel H., Kel A.E., Wingender E. TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res. 2006, 34:D108-D110.
20. Podvinec M., Kaufmann M.R., Handschin C., Meyer U.A. NUBIScan, an in silico approach for prediction of nuclear receptor response elements. Mol. Endocrinol. 2002, 16:1269-1279.
21. Sandelin A., Wasserman W.W. Prediction of nuclear hormone receptor response elements. Mol. Endocrinol. 2005, 19:595-606.
22. Fang H.L., Strom S.C., Cai H., Falany C.N., Kocarek T.A., Runge-Morris M. Regulation of human hepatic hydroxysteroid sulfotransferase gene expression by the peroxisome proliferator-activated receptor alpha transcription factor. Mol. Pharmacol. 2005, 67:1257-1267.
23. Pineda Torra I., Jamshidi Y., Flavell D.M., Fruchart J.C., Staels B. Characterization of the human PPARalpha promoter: identification of a functional nuclear receptor response element. Mol. Endocrinol. 2002, 16:1013-1028.
24. Tang C., Cho H.P., Nakamura M.T., Clarke S.D. Regulation of human delta-6 desaturase gene transcription: identification of a functional direct repeat-1 element. J. Lipid Res. 2003, 44:686-695.
25. Targett-Adams P., McElwee M.J., Ehrenborg E., Gustafsson M.C., Palmer C.N., McLauchlan J. A PPAR response element regulates transcription of the gene for human adipose differentiation-related protein. Biochim. Biophys. Acta 2005, 1728:95-104.
26. Sher T., Yi H.F., McBride O.W., Gonzalez F.J. cDNA cloning, chromosomal mapping, and functional characterization of the human peroxisome proliferator activated receptor. Biochemistry 1993, 32:5598-5604.
27. Palmer C.N.A., Hsu M.H., Griffin K.J., Johnson E.F. Novel sequence determinants in peroxisome proliferator signaling. J. Biol. Chem. 1995, 270:16,114-16,121.
28. Gurevich I., Zhang C., Aneskievich B.J. Scanning for transcription factor binding by a variant EMSA. Methods Mol. Biol. 2010, 585:147-158.
29. Nowak D.E., Tian B., Brasier A.R. Two-step cross-linking method for identification of NF-kappaB gene network by chromatin immunoprecipitation. Biotechniques 2005, 39:715-725.
30. Gillespie R.F., Gudas L.J. Retinoid regulated association of transcriptional co-regulators and the polycomb group protein SUZ12 with the retinoic acid response elements of Hoxa1, RARbeta(2), and Cyp26A1 in F9 embryonal carcinoma cells. J. Mol. Biol. 2007, 372:298-316.
31. Eeckhoute J., Carroll J.S., Geistlinger T.R., Torres-Arzayus M.I., Brown M. A cell-type-specific transcriptional network required for estrogen regulation of cyclin D1 and cell cycle progression in breast cancer. Genes Dev. 2006, 20:2513-2526.
32. Munoz E., Courtois G., Veschambre P., Jalinot P., Israel A. Tax induces nuclear translocation of NF-kappa B through dissociation of cytoplasmic complexes containing p105 or p100 but does not induce degradation of I kappa B alpha/MAD3. J. Virol. 1994, 68:8035-8044.
33. Smale S.T., Kadonaga J.T. The RNA polymerase II core promoter. Annu. Rev. Biochem. 2003, 72:449-479.
34. Carninci P., Sandelin A., Lenhard B., Katayama S., Shimokawa K., Ponjavic J., Semple C.A., Taylor M.S., Engstrom P.G., Frith M.C., Forrest A.R., Alkema W.B., Tan S.L., Plessy C., Kodzius R., Ravasi T., Kasukawa T., Fukuda S., Kanamori-Katayama M., Kitazume Y., Kawaji H., Kai C., Nakamura M., Konno H., Nakano K., Mottagui-Tabar S., Arner P., Chesi A., Gustincich S., Persichetti F., Suzuki H., Grimmond S.M., Wells C.A., Orlando V., Wahlestedt C., Liu E.T., Harbers M., Kawai J., Bajic V.B., Hume D.A., Hayashizaki Y. Genome-wide analysis of mammalian promoter architecture and evolution. Nat. Genet. 2006, 38:626-635.
35. Kawaji H., Kasukawa T., Fukuda S., Katayama S., Kai C., Kawai J., Carninci P., Hayashizaki Y. CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis. Nucleic Acids Res. 2006, 34:D632-D636.
36. Favre M., Butticaz C., Stevenson B., Jongeneel C.V., Telenti A. High frequency of alternative splicing of human genes participating in the HIV-1 life cycle: a model using TSG101, betaTrCP, PPIA, INI1, NAF1, and PML. J. Acquir. Immune Defic. Syndr. 2003, 34:127-133.
37. Hayes M.M., Lane B.R., King S.R., Markovitz D.M., Coffey M.J. Peroxisome proliferator-activated receptor gamma agonists inhibit HIV-1 replication in macrophages by transcriptional and post-transcriptional effects. J. Biol. Chem. 2002, 277:16913-16919.
38. Wang C., Fu M., D'Amico M., Albanese C., Zhou J.N., Brownlee M., Lisanti M.P., Chatterjee V.K., Lazar M.A., Pestell R.G. Inhibition of cellular proliferation through IkappaB kinase-independent and peroxisome proliferator-activated receptor gamma-dependent repression of cyclin D1. Mol. Cell. Biol. 2001, 21:3057-3070.
39. Straus D.S., Pascual G., Li M., Welch J.S., Ricote M., Hsiang C.H., Sengchanthalangsy L.L., Ghosh G., Glass C.K. 15-deoxy-delta 12,14-prostaglandin J2 inhibits multiple steps in the NF-kappa B signaling pathway. Proc. Natl. Acad. Sci. U. S. A. 2000, 97:4844-4849.
40. Nielsen R., Grontved L., Stunnenberg H.G., Mandrup S. Peroxisome proliferator-activated receptor subtype- and cell-type-specific activation of genomic target genes upon adenoviral transgene delivery. Mol. Cell. Biol. 2006, 26:5698-5714.
41. Song S., Attia R.R., Connaughton S., Niesen M.I., Ness G.C., Elam M.B., Hori R.T., Cook G.A., Park E.A. Peroxisome proliferator activated receptor alpha (PPARalpha) and PPAR gamma coactivator (PGC-1alpha) induce carnitine palmitoyltransferase IA (CPT-1A) via independent gene elements. Mol. Cell. Endocrinol. 2010, 325:54-63.
42. Hauser S., Adelmant G., Sarraf P., Wright H.M., Mueller E., Spiegelman B.M. Degradation of the peroxisome proliferator-activated receptor gamma is linked to ligand-dependent activation. J. Biol. Chem. 2000, 275:18527-18533.
43. Delacroix L., Begon D., Chatel G., Jackers P., Winkler R. Distal ERBB2 promoter fragment displays specific transcriptional and nuclear binding activities in ERBB2 overexpressing breast cancer cells. DNA Cell Biol. 2005, 24:582-594.
44. Helledie T., Grontved L., Jensen S.S., Kiilerich P., Rietveld L., Albrektsen T., Boysen M.S., Nohr J., Larsen L.K., Fleckner J., Stunnenberg H.G., Kristiansen K., Mandrup S. The gene encoding the Acyl-CoA-binding protein is activated by peroxisome proliferator-activated receptor gamma through an intronic response element functionally conserved between humans and rodents. J. Biol. Chem. 2002, 277:26821-26830.
45. Basu-Modak S., Braissant O., Escher P., Desvergne B., Honegger P., Wahli W. Peroxisome proliferator-activated receptor beta regulates acyl-CoA synthetase 2 in reaggregated rat brain cell cultures. J. Biol. Chem. 1999, 274:35881-35888.
46. Dean J., Plante J., Huggins G.S., Snyder R.O., Aikawa R. Role of cyclic AMP-dependent kinase response element-binding protein in recombinant adeno-associated virus-mediated transduction of heart muscle cells. Hum. Gene Ther. 2009, 20:1005-1012.
47. Tachibana K., Kobayashi Y., Tanaka T., Tagami M., Sugiyama A., Katayama T., Ueda C., Yamasaki D., Ishimoto K., Sumitomo M., Uchiyama Y., Kohro T., Sakai J., Hamakubo T., Kodama T., Doi T. Gene expression profiling of potential peroxisome proliferator-activated receptor (PPAR) target genes in human hepatoblastoma cell lines inducibly expressing different PPAR isoforms. Nucl. Recept. 2005, 3:3.
48. Fernandes I., Bastien Y., Wai T., Nygard K., Lin R., Cormier O., Lee H.S., Eng F., Bertos N.R., Pelletier N., Mader S., Han V.K., Yang X.J., White J.H. Ligand-dependent nuclear receptor corepressor LCoR functions by histone deacetylase-dependent and -independent mechanisms. Mol. Cell 2003, 11:139-150.
49. Fritah A., Christian M., Parker M.G. The metabolic coregulator RIP140: an update. Am. J. Physiol. Endocrinol. Metab. 2010, 299:E335-E340.
50. Lee D.D., Stojadinovic O., Krzyzanowska A., Vouthounis C., Blumenberg M., Tomic-Canic M. Retinoid-responsive transcriptional changes in epidermal keratinocytes. J. Cell. Physiol. 2009, 220:427-439.
51. Wullaert A., Wielockx B., Van Huffel S., Bogaert V., De Geest B., Papeleu P., Schotte P., El Bakkouri K., Heyninck K., Libert C., Beyaert R. Adenoviral gene transfer of ABIN-1 protects mice from TNF/galactosamine-induced acute liver failure and lethality. Hepatology 2005, 42:381-389.
52. El Bakkouri K., Wullaert A., Haegman M., Heyninck K., Beyaert R. Adenoviral gene transfer of the NF-kappa B inhibitory protein ABIN-1 decreases allergic airway inflammation in a murine asthma model. J. Biol. Chem. 2005, 280:17938-17944.
53. Gallagher J., Howlin J., McCarthy C., Murphy E.P., Bresnihan B., FitzGerald O., Godson C., Brady H.R., Martin F. Identification of Naf1/ABIN-1 among TNF-alpha-induced expressed genes in human synoviocytes using oligonucleotide microarrays. FEBS Lett. 2003, 551:8-12.
54. Kostadinova R., Wahli W., Michalik L. PPARs in diseases: control mechanisms of inflammation. Curr. Med. Chem. 2005, 12:2995-3009.
55. Molnar F., Matilainen M., Carlberg C. Structural determinants of the agonist-independent association of human peroxisome proliferator-activated receptors with coactivators. J. Biol. Chem. 2005, 280:26543-26556.
56. Adhikary T., Kaddatz K., Finkernagel F., Schonbauer A., Meissner W., Scharfe M., Jarek M., Blocker H., Muller-Brusselbach S., Muller R. Genomewide analyses define different modes of transcriptional regulation by peroxisome proliferator-activated receptor-beta/delta (PPARbeta/delta). PLoS One 2011, 6:e16344.
57. Shimizu M., Yamashita D., Yamaguchi T., Hirose F., Osumi T. Aspects of the regulatory mechanisms of PPAR functions: analysis of a bidirectional response element and regulation by sumoylation. Mol. Cell. Biochem. 2006, 286:33-42.
58. Nolte R.T., Wisely G.B., Westin S., Cobb J.E., Lambert M.H., Kurokawa R., Rosenfeld M.G., Willson T.M., Glass C.K., Milburn M.V. Ligand binding and co-activator assembly of the peroxisome proliferator-activated receptor-gamma. Nature 1998, 395:137-143.
59. Todorov V.T., Desch M., Schmitt-Nilson N., Todorova A., Kurtz A. Peroxisome proliferator-activated receptor-gamma is involved in the control of renin gene expression. Hypertension 2007, 50:939-944.
60. Okuno M., Arimoto E., Ikenobu Y., Nishihara T., Imagawa M. Dual DNA-binding specificity of peroxisome-proliferator-activated receptor gamma controlled by heterodimer formation with retinoid X receptor alpha. Biochem. J. 2001, 353:193-198.
61. Wang C., Mayer J.A., Mazumdar A., Fertuck K., Kim H., Brown M., Brown P.H. Estrogen Induces c-myc Gene Expression via an Upstream Enhancer Activated by the Estrogen Receptor and the AP-1 Transcription Factor. Mol. Endocrinol. 2011, 25:1527-1538.
62. Durand B., Saunders M., Leroy P., Leid M., Chambon P. All-trans and 9-cis retinoic acid induction of CRABPII transcription is mediated by RAR-RXR heterodimers bound to DR1 and DR2 repeated motifs. Cell 1992, 71:73-85.
63. Chan L.S., Wells R.A. Cross-Talk between PPARs and the Partners of RXR: A Molecular Perspective. PPAR Res 2009, 2009:925309.
64. Lee H.K., Park U.H., Kim E.J., Um S.J. MED25 is distinct from TRAP220/MED1 in cooperating with CBP for retinoid receptor activation. EMBO J. 2007, 26:3545-3557.
65. Keriel A., Stary A., Sarasin A., Rochette-Egly C., Egly J.M. XPD mutations prevent TFIIH-dependent transactivation by nuclear receptors and phosphorylation of RARalpha. Cell 2002, 109:125-135.
66. De Bosscher K., Vanden Berghe W., Haegeman G. Cross-talk between nuclear receptors and nuclear factor kappaB. Oncogene 2006, 25:6868-6886.
67. Zou F., Liu Y., Liu L., Wu K., Wei W., Zhu Y., Wu J. Retinoic acid activates human inducible nitric oxide synthase gene through binding of RARalpha/RXRalpha heterodimer to a novel retinoic acid response element in the promoter. Biochem. Biophys. Res. Commun. 2007, 355:494-500.
68. Toell A., Kroncke K.D., Kleinert H., Carlberg C. Orphan nuclear receptor binding site in the human inducible nitric oxide synthase promoter mediates responsiveness to steroid and xenobiotic ligands. J. Cell. Biochem. 2002, 85:72-82.
69. Saavalainen K., Tammi M.I., Bowen T., Schmitz M.L., Carlberg C.M. Integration of the activation of the human hyaluronan synthase 2 gene promoter by common cofactors of the transcription factors retinoic acid receptor and nuclear factor kappaB. J. Biol. Chem. 2007, 282:11530-11539.
70. Alvarez M., Rhodes S.J., Bidwell J.P. Context-dependent transcription: all politics is local. Gene 2003, 313:43-57.
71. Li M., Pascual G., Glass C.K. Peroxisome proliferator-activated receptor gamma-dependent repression of the inducible nitric oxide synthase gene. Mol. Cell. Biol. 2000, 20:4699-4707.
72. Chung S.W., Kang B.Y., Kim S.H., Pak Y.K., Cho D., Trinchieri G., Kim T.S. Oxidized low density lipoprotein inhibits interleukin-12 production in lipopolysaccharide-activated mouse macrophages via direct interactions between peroxisome proliferator-activated receptor-gamma and nuclear factor-kappa B. J. Biol. Chem. 2000, 275:32681-32687.
73. Rochette-Egly C. Dynamic combinatorial networks in nuclear receptor-mediated transcription. J. Biol. Chem. 2005, 280:32565-32568.
74. Engelhard A., Bauer R.C., Casta A., Djabali K., Christiano A.M. Ligand-independent regulation of the hairless promoter by vitamin D receptor. Photochem. Photobiol. 2008, 84:515-521.
75. White R., Morganstein D., Christian M., Seth A., Herzog B., Parker M.G. Role of RIP140 in metabolic tissues: connections to disease. FEBS Lett. 2008, 582:39-45.
76. Werner S.L., Kearns J.D., Zadorozhnaya V., Lynch C., O'Dea E., Boldin M.P., Ma A., Baltimore D., Hoffmann A. Encoding NF-kappaB temporal control in response to TNF: distinct roles for the negative regulators IkappaBalpha and A20. Genes Dev. 2008, 22:2093-2101.
77. Ausubel F.M., Brent R., Kingston R.E., Moore D.D., Seidman J.G., Smith J.A., Struhl K. Current Protocols in Molecular Biology 2004, J. Wiley.
78. Bruggeman L.A., Adler S.H., Klotman P.E. Nuclear factor-kappa B binding to the HIV-1 LTR in kidney: implications for HIV-associated nephropathy. Kidney Int. 2001, 59:2174-2181.