Abstract
Inflammatory responses to microbial and non-microbial stimuli involve coordinate changes in the expression of hundreds of genes. The inflammatory gene expression programs display two important features: first, alternative stimuli affect both a large set of common genes and a variable number of stimulus-specific genes. Second, different genes are activated with different kinetics over several hours after the initial stimulus. Mechanistically, these features reflect the interplay between two main groups of determinants: the combinatorial control of transcription by multiple transcription factors, with NF-κB and the IRFs playing a central and essential role in the induction of a large fraction of inflammatory genes; and the presence of well-defined, in part cell-type specific, patterns of chromatin organization at cis-regulatory regions of inflammatory genes. Recent advancements in this field are providing paradigms of general value explaining how inducible responses to environmental stimuli are controlled.
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Angelov D, Lenouvel F, Hans F, Muller CW, Bouvet P, Bednar J, Moudrianakis EN, Cadet J, Dimitrov S (2004) The histone octamer is invisible when NF-kappaB binds to the nucleosome. J Biol Chem 279:42374–42382
Ayton PM, Chen EH, Cleary ML (2004) Binding to nonmethylated CpG DNA is essential for target recognition, transactivation, and myeloid transformation by an MLL oncoprotein. Mol Cell Biol 24:10470–10478
Boeger H, Griesenbeck J, Kornberg RD (2008) Nucleosome retention and the stochastic nature of promoter chromatin remodeling for transcription. Cell 133:716–726
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
Covert MW, Leung TH, Gaston JE, Baltimore D (2005) Achieving stability of lipopolysaccharide-induced NF-kappaB activation. Science 309:1854–1857
Doyle S, Vaidya S, O’Connell R, Dadgostar H, Dempsey P, Wu T, Rao G, Sun R, Haberland M, Modlin R, Cheng G (2002) IRF3 mediates a TLR3/TLR4-specific antiviral gene program. Immunity 17:251–263
Hargreaves DC, Horng T, Medzhitov R (2009) Control of inducible gene expression by signal-dependent transcriptional elongation. Cell 138:129–145
Hoffmann A, Levchenko A, Scott ML, Baltimore D (2002) The IkappaB-NF-kappaB signaling module: temporal control and selective gene activation. Science 298:1241–1245
Huxford T, Malek S, Ghosh G (1999) Structure and mechanism in NF-kappa B/I kappa B signaling. Cold Spring Harb Symp Quant Biol 64:533–540
Janeway CA Jr, Medzhitov R (2002) Innate immune recognition. Annu Rev Immunol 20:197–216
Jiang C, Pugh BF (2009) Nucleosome positioning and gene regulation: advances through genomics. Nat Rev Genet 10:161–172
Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, Field Y, Leproust EM, Hughes TR, Lieb JD, Widom J, Segal E (2008) The DNA-encoded nucleosome organization of a eukaryotic genome. Nature 458:362–366.
Kayama H, Ramirez-Carrozzi VR, Yamamoto M, Mizutani T, Kuwata H, Iba H, Matsumoto M, Honda K, Smale ST, Takeda K (2008) Class-specific regulation of pro-inflammatory genes by MyD88 pathways and IkappaBzeta. J Biol Chem 283:12468–12477
Lee JH, Skalnik DG (2005) CpG-binding protein (CXXC finger protein 1) is a component of the mammalian Set1 histone H3-Lys4 methyltransferase complex, the analogue of the yeast Set1/COMPASS complex. J Biol Chem 280:41725–41731
Lee JH, Skalnik DG (2008) Wdr82 is a C-terminal domain-binding protein that recruits the Setd1A Histone H3-Lys4 methyltransferase complex to transcription start sites of transcribed human genes. Mol Cell Biol 28:609–618
Mavrich TN, Ioshikhes IP, Venters BJ, Jiang C, Tomsho LP, Qi J, Schuster SC, Albert I, Pugh BF (2008) A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Res 18:1073–1083
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
Nau GJ, Richmond JF, Schlesinger A, Jennings EG, Lander ES, Young RA (2002) Human macrophage activation programs induced by bacterial pathogens. Proc Natl Acad Sci USA 99:1503–1508
Phatnani HP, Greenleaf AL (2006) Phosphorylation and functions of the RNA polymerase II CTD. Genes Dev 20:2922–2936
Ponting CP (2008) The functional repertoires of metazoan genomes. Nat Rev Genet 9:689–698
Ramirez-Carrozzi VR, Braas D, Bhatt DM, Cheng CS, Hong C, Doty KR, Black JC, Hoffmann A, Carey M, Smale ST (2009) A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling. Cell 138:114–128
Ramirez-Carrozzi VR, Nazarian AA, Li CC, Gore SL, Sridharan R, Imbalzano AN, Smale ST (2006) Selective and antagonistic functions of SWI/SNF and Mi-2beta nucleosome remodeling complexes during an inflammatory response. Genes Dev 20:282–296
Saccani S, Pantano S, Natoli G (2001) Two waves of nuclear factor kappaB recruitment to target promoters. J Exp Med 193:1351–1359
Saccani S, Pantano S, Natoli G (2002) p38-Dependent marking of inflammatory genes for increased NF-kappa B recruitment. Nat Immunol 3:69–75
Segal E, Fondufe-Mittendorf Y, Chen L, Thastrom A, Field Y, Moore IK, Wang JP, Widom J (2006) A genomic code for nucleosome positioning. Nature 442:772–778
Shilatifard A (2006) Chromatin modifications by methylation and ubiquitination: implications in the regulation of gene expression. Annu Rev Biochem 75:243–269
Toshchakov V, Jones BW, Perera PY, Thomas K, Cody MJ, Zhang S, Williams BR, Major J, Hamilton TA, Fenton MJ, Vogel SN (2002) TLR4, but not TLR2, mediates IFN-beta-induced STAT1alpha/beta-dependent gene expression in macrophages. Nat Immunol 3:392–398
Werner SL, Barken D, Hoffmann A (2005) Stimulus specificity of gene expression programs determined by temporal control of IKK activity. Science 309:1857–1861
Acknowledgments
Research in GN lab is supported by the EC FP6 programme (Marie Curie excellence grant Trans-Tar), the FP7 programme (integrated project Model-In) and the Italian Association for Research on Cancer (A.I.R.C.).
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Natoli, G. (2010). Specialized Chromatin Patterns in the Control of Inflammatory Gene Expression. In: Karin, M. (eds) NF-kB in Health and Disease. Current Topics in Microbiology and Immunology, vol 349. Springer, Berlin, Heidelberg. https://doi.org/10.1007/82_2010_106
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DOI: https://doi.org/10.1007/82_2010_106
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