Two modes of transcriptional activation at native promoters by NF-κB p65

PLoS Biology

Volumn 7, Issue 3, 2009, Pages 0549-0562

  Essen, Dominic Van ^a   Engist, Bettina ^a   Natoli, Gioacchino ^b   Saccani, Simona ^a  

^a MAX PLANCK INSTITUTE OF IMMUNOBIOLOGY AND EPIGENETICS   (Germany)

^b EUROPEAN INSTITUTE OF ONCOLOGY   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR RELA;

ARTICLE; CONTROLLED STUDY; GENE TARGETING; GENETIC TRANSCRIPTION; HUMAN; HUMAN CELL; PROTEIN EXPRESSION; PROTEIN PROTEIN INTERACTION;

EID: 65949089152     PISSN: 15449173     EISSN: 15457885     Source Type: Journal    
DOI: 10.1371/journal.pbio.1000073     Document Type: Article

References (53)

1. Hoffmann A, Baltimore D (2006) Circuitry of nuclear factor kappaB signaling. Immunol Rev 210: 171-186.
2. Natoli G, Saccani S, Bosisio D, Marazzi I (2005) Interactions of NF-kappaB with chromatin: the art of being at the right place at the right time. Nat Immunol 6: 439-445.
3. Orphanides G, Lagrange T, Reinberg D (1996) The general transcription factors of RNA polymerase II. Genes Dev 10: 2657-2683.
4. Malik S, Roeder RG (2005) Dynamic regulation of pol II transcription by the mammalian Mediator complex. Trends Biochem Sci 30: 256-263.
5. Guermah M, Tao Y, Roeder RG (2001) Positive and negative TAF(II) functions that suggest a dynamic TFIID structure and elicit synergy with traps in activator-induced transcription. Mol Cell Biol 21: 6882-6894.
6. Acevedo ML, Kraus WL (2003) Mediator and p300/CBP-steroid receptor coactivator complexes have distinct roles, but function synergistically, during estrogen receptor alpha-dependent transcription with chromatin templates. Mol Cell Biol 23: 335-348.
7. Mittler G, Kremmer E, Timmers HT, Meisterernst M (2001) Novel critical role of a human Mediator complex for basal RNA polymerase II transcription. EMBO Rep 2: 808-813.
8. Ballard DW, Dixon EP, Peffer NJ, Bogerd H, Doerre S, et al. (1992) The 65- kDa subunit of human NF-kappa B functions as a potent transcriptional activator and a target for v-Rel-mediated repression. Proc Natl Acad Sci U S A 89: 1875-1879.
9. Schmitz ML, Baeuerle PA (1991) The p65 subunit is responsible for the strong transcription activating potential of NF-kappa B. Embo J 10: 3805-3817.
10. Naar AM, Beaurang PA, Zhou S, Abraham S, Solomon W, et al. (1999) Composite co-activator ARC mediates chromatin-directed transcriptional activation. Nature 398: 828-832.
11. Kim TW, Kwon YJ, Kim JM, Song YH, Kim SN, et al. (2004) MED16 and MED23 of Mediator are coactivators of lipopolysaccharide- and heat-shock-induced transcriptional activators. Proc Natl Acad Sci U S A 101: 12153-12158.
12. Boube M, Joulia L, Cribbs DL, Bourbon HM (2002) Evidence for a mediator of RNA polymerase II transcriptional regulation conserved from yeast to man. Cell 110: 143-151.
13. Hu CD, Chinenov Y, Kerppola TK (2002) Visualization of interactions among bZIP and Rel family proteins in living cells using bimolecular fluorescence complementation. Mol Cell 9: 789-798.
14. Chen FE, Huang DB, Chen YQ, Ghosh G (1998) Crystal structure of p50/p65 heterodimer of transcription factor NF-kappaB bound to DNA. Nature 391: 410-413.
15. Holstege FC, Jennings EG, Wyrick JJ, Lee TI, Hengartner CJ, et al. (1998) Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95: 717-728.
16. Thompson CM, Young RA (1995) General requirement for RNA polymer- ase II holoenzymes in vivo. Proc Natl Acad Sci U S A 92: 4587-4590.
17. Boube M, Faucher C, Joulia L, Cribbs DL, Bourbon HM (2000) Drosophila homologs of transcriptional mediator complex subunits are required for adult cell and segment identity specification. Genes Dev 14: 2906-2917.
18. Hoffmann A, Leung TH, Baltimore D (2003) Genetic analysis of NF-kappaB/Rel transcription factors defines functional specificities. Embo J 22: 5530-5539.
19. Ouaaz F, Li M, Beg AA (1999) A critical role for the RelA subunit of nuclear factor kappaB in regulation of multiple immune-response genes and in Fas-induced cell death. J Exp Med 189: 999-1004.
20. Ranish JA, Yudkovsky N, Hahn S (1999) Intermediates in formation and activity of the RNA polymerase II preinitiation complex: holoenzyme recruitment and a postrecruitment role for the TATA box and TFIIB. Genes Dev 13: 49-63.
21. Malik S, Gu W, Wu W, Qin J, Roeder RG (2000) The USA-derived transcriptional coactivator PC2 is a submodule of TRAP/SMCC and acts synergistically with other PCs. Mol Cell 5: 753-760.
22. Naar AM, Taatjes DJ, Zhai W, Nogales E, Tjian R (2002) Human CRSP interacts with RNA polymerase II CTD and adopts a specific CTD-bound conformation. Genes Dev 16: 1339-1344.
23. Sato S, Tomomori-Sato C, Parmely TJ, Florens L, Zybailov B, et al. (2004) A set of consensus mammalian mediator subunits identified by multidimen- sional protein identification technology. Mol Cell 14: 685-691.
24. Taatjes DJ, Naar AM, Andel F 3rd, Nogales E, Tjian R (2002) Structure, function, and activator-induced conformations of the CRSP coactivator. Science 295: 1058-1062.
25. Andrau JC, van de Pasch L, Lijnzaad P, Bijma T, Koerkamp MG, et al. (2006) Genome-wide location of the coactivator mediator: Binding without activation and transient Cdk8 interaction on DNA. Mol Cell 22: 179-192.
26. Mittler G, Stuhler T, Santolin L, Uhlmann T, Kremmer E, et al. (2003) A novel docking site on Mediator is critical for activation by VP16 in mammalian cells. Embo J 22: 6494-6504.
27. Marin M, Karis A, Visser P, Grosveld F, Philipsen S (1997) Transcription factor Sp1 is essential for early embryonic development but dispensable for cell growth and differentiation. Cell 89: 619-628.
28. Ping D, Boekhoudt G, Zhang F, Morris A, Philipsen S, et al. (2000) Sp1 binding is critical for promoter assembly and activation of the MCP-1 gene by tumor necrosis factor. J Biol Chem 275: 1708-1714.
29. Ryu S, Zhou S, Ladurner AG, Tjian R (1999) The transcriptional cofactor complex CRSP is required for activity of the enhancer-binding protein Sp1. Nature 397: 446-450.
30. Chen JL, Attardi LD, Verrijzer CP, Yokomori K, Tjian R (1994) Assembly of recombinant TFIID reveals differential coactivator requirements for distinct transcriptional activators. Cell 79: 93-105.
31. Kim TH, Barrera LO, Zheng M, Qu C, Singer MA, et al. (2005) A high- resolution map of active promoters in the human genome. Nature 436: 876-880.
32. Kuras L, Kosa P, Mencia M, Struhl K (2000) TAF-Containing and TAF- independent forms of transcriptionally active TBP in vivo. Science 288: 1244-1248.
33. Li XY, Bhaumik SR, Green MR (2000) Distinct classes of yeast promoters revealed by differential TAF recruitment. Science 288: 1242-1244.
34. Walker SS, Shen WC, Reese JC, Apone LM, Green MR (1997) Yeast TAF(II)145 required for transcription of G1/S cyclin genes and regulated by the cellular growth state. Cell 90: 607-614.
35. Wang EH, Tjian R (1994) Promoter-selective transcriptional defect in cell cycle mutant ts13 rescued by hTAFII250. Science 263: 811-814.
36. Linder T, Zhu X, Baraznenok V, Gustafsson CM (2006) The classical srb4-138 mutant allele causes dissociation of yeast Mediator. Biochem Biophys Res Commun 349: 948-953.
37. Takagi Y, Calero G, Komori H, Brown JA, Ehrensberger AH, et al. (2006) Head module control of mediator interactions. Mol Cell 23: 355-364.
38. Baek HJ, Malik S, Qin J, Roeder RG (2002) Requirement of TRAP/mediator for both activator-independent and activator-dependent transcription in conjunction with TFIID-associated TAF(II)s. Mol Cell Biol 22: 2842-2852.
39. Paoletti AC, Parmely TJ, Tomomori-Sato C, Sato S, Zhu D, et al. (2006) Quantitative proteomic analysis of distinct mammalian Mediator com- plexes using normalized spectral abundance factors. Proc Natl Acad Sci U S A 103: 18928-18933.
40. Perkins ND, Agranoff AB, Pascal E, Nabel GJ (1994) An interaction between the DNA-binding domains of RelA(p65) and Sp1 mediates human immunodeficiency virus gene activation. Mol Cell Biol 14: 6570-6583.
41. Thanos D, Maniatis T (1995) Virus induction of human IFN beta gene expression requires the assembly of an enhanceosome. Cell 83: 1091-1100.
42. Ramirez-Carrozzi VR, Nazarian AA, Li CC, Gore SL, Sridharan R, et al. (2006) Selective and antagonistic functions of SWI/SNF and Mi-2beta nucleosome remodeling complexes during an inflammatory response. Genes Dev 20: 282-296.
43. Boekhoudt GH, Guo Z, Beresford GW, Boss JM (2003) Communication between NF-kappa B and Sp1 controls histone acetylation within the proximal promoter of the monocyte chemoattractant protein 1 gene. J Immunol 170: 4139-4147.
44. Dong J, Jimi E, Zhong H, Hayden MS, Ghosh S (2008) Repression of gene expression by unphosphorylated NF-kappaB p65 through epigenetic mechanisms. Genes Dev 22: 1159-1173.
45. Saccani S, Natoli G (2002) Dynamic changes in histone H3 Lys 9 methylation occurring at tightly regulated inducible inflammatory genes. Genes Dev 16: 2219-2224.
46. Anest V, Hanson JL, Cogswell PC, Steinbrecher KA, Strahl BD, et al. (2003) A nucleosomal function for IkappaB kinase-alpha in NF-kappaB-depend- ent gene expression. Nature 423: 659-663.
47. Yamamoto Y, Verma UN, Prajapati S, Kwak YT, Gaynor RB (2003) Histone H3 phosphorylation by IKK-alpha is critical for cytokine-induced gene expression. Nature 423: 655-659.
48. Arenzana-Seisdedos F, Thompson J, Rodriguez MS, Bachelerie F, Thomas D, et al. (1995) Inducible nuclear expression of newly synthesized I kappa B alpha negatively regulates DNA-binding and transcriptional activities of NF-kappa B. Mol Cell Biol 15: 2689-2696.
49. Saccani S, Marazzi I, Beg AA, Natoli G (2004) Degradation of promoter- bound p65/RelA is essential for the prompt termination of the nuclear factor kappaB response. J Exp Med 200: 107-113.
50. Saccani S, Pantano S, Natoli G (2003) Modulation of NF-kappaB activity by exchange of dimers. Mol Cell 11: 1563-1574.
51. Sandelin A, Wasserman WW, Lenhard B (2004) ConSite: web-based prediction of regulatory elements using cross-species comparison. Nucleic Acids Res 32: W249-W252.
52. Thijs G, Lescot M, Marchal K, Rombauts S, De Moor B, et al. (2001) A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling. Bioinformatics 17: 1113-1122.
53. Saccani S, Pantano S, Natoli G (2001) Two waves of nuclear factor kappaB recruitment to target promoters. J Exp Med 193: 1351-1359.