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The stability of mRNA influences the temporal order of the induction of genes encoding inflammatory molecules

Abstract

The inflammatory response plays out over time in a reproducible and organized way after an initiating stimulus. Here we show that genes activated in cultured mouse fibroblasts in response to the cytokine tumor necrosis factor could be categorized into roughly three groups, each with different induction kinetics. Although differences in transcription were important in determining the grouping of these genes, differences in mRNA stability also exerted a strong influence on the temporal order of gene expression, in some cases overriding that of transcriptional control elements. Transcripts of mRNA expressed early had abundant AU-rich elements in their 3′ untranslated regions, whereas those expressed later had fewer. Thus, mRNA stability and transcriptional control, two intrinsic characteristics of genes, control the kinetics of gene expression induced by proinflammatory cytokines.

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Figure 1: TNF-activated genes can be categorized into three kinetically different groups.
Figure 2: Gene expression after TNF withdrawal.
Figure 3: Stability of mRNA encoded by genes in groups I, II and III.
Figure 4: Kinetic patterns of gene expression in macrophages.
Figure 5: Gene-expression patterns are determined by the 3′ UTR of a gene.

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References

  1. Majno, G. The Healing Hand: Man and Wound in the Ancient World (Harvard University Press, Cambridge, 1975).

    Google Scholar 

  2. Stramer, B.M., Mori, R. & Martin, P. The inflammation-fibrosis link? A Jekyll and Hyde role for blood cells during wound repair. J. Invest. Dermatol. 127, 1009–1017 (2007).

    Article  CAS  PubMed  Google Scholar 

  3. Bradley, J.R. TNF-mediated inflammatory disease. J. Pathol. 214, 149–160 (2008).

    Article  CAS  PubMed  Google Scholar 

  4. Beg, A.A. & Baltimore, D. An essential role for NF-κB in preventing TNF-α-induced cell death. Science 274, 782–784 (1996).

    Article  CAS  PubMed  Google Scholar 

  5. Hoffmann, A., Leung, T.H. & Baltimore, D. Genetic analysis of NF-κB/Rel transcription factors defines functional specificities. EMBO J. 22, 5530–5539 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Tian, B., Nowak, D.E., Jamaluddin, M., Wang, S. & Brasier, A.R. Identification of direct genomic targets downstream of the nuclear factor-κB transcription factor mediating tumor necrosis factor signaling. J. Biol. Chem. 280, 17435–17448 (2005).

    Article  CAS  PubMed  Google Scholar 

  7. Viemann, D. et al. TNF induces distinct gene expression programs in microvascular and macrovascular human endothelial cells. J. Leukoc. Biol. 80, 174–185 (2006).

    Article  CAS  PubMed  Google Scholar 

  8. Zhao, B., Stavchansky, S.A., Bowden, R.A. & Bowman, P.D. Effect of interleukin-1β and tumor necrosis factor-α on gene expression in human endothelial cells. Am. J. Physiol. Cell Physiol. 284, C1577–C1583 (2003).

    Article  CAS  PubMed  Google Scholar 

  9. Schwamborn, J. et al. Microarray analysis of tumor necrosis factor α induced gene expression in U373 human glioblastoma cells. BMC Genomics 4, 46 (2003).

    Article  PubMed  PubMed Central  Google Scholar 

  10. Karin, M., Cao, Y., Greten, F.R. & Li, Z.W. NF-κB in cancer: from innocent bystander to major culprit. Nat. Rev. Cancer 2, 301–310 (2002).

    Article  CAS  PubMed  Google Scholar 

  11. Li, X. et al. IKKα, IKKβ, and NEMO/IKKγ are each required for the NF-κB-mediated inflammatory response program. J. Biol. Chem. 277, 45129–45140 (2002).

    Article  CAS  PubMed  Google Scholar 

  12. Hartigan, J.A. Clustering Algorithm (John Wiley and Sons, New York, 1975).

  13. Wilson, T. & Treisman, R. Removal of poly(A) and consequent degradation of c-fos mRNA facilitated by 3′ AU-rich sequences. Nature 336, 396–399 (1988).

    Article  CAS  PubMed  Google Scholar 

  14. Franklin, R.M. & Baltimore, D. Patterns of macromolecular synthesis in normal and virus-infected mammalian cells. Cold Spring Harb. Symp. Quant. Biol. 27, 175–198 (1962).

    Article  CAS  PubMed  Google Scholar 

  15. Carballo, E., Lai, W.S. & Blackshear, P.J. Feedback inhibition of macrophage tumor necrosis factor-α production by tristetraprolin. Science 281, 1001–1005 (1998).

    Article  CAS  PubMed  Google Scholar 

  16. Lai, W.S. et al. Evidence that tristetraprolin binds to AU-rich elements and promotes the deadenylation and destabilization of tumor necrosis factor α mRNA. Mol. Cell. Biol. 19, 4311–4323 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Sauer, I. et al. Interferons limit inflammatory responses by induction of tristetraprolin. Blood 107, 4790–4797 (2006).

    Article  CAS  PubMed  Google Scholar 

  18. Amit, I. et al. A module of negative feedback regulators defines growth factor signaling. Nat. Genet. 39, 503–512 (2007).

    Article  CAS  PubMed  Google Scholar 

  19. Shim, J. & Karin, M. The control of mRNA stability in response to extracellular stimuli. Mol. Cells 14, 323–331 (2002).

    CAS  PubMed  Google Scholar 

  20. Han, J., Brown, T. & Beutler, B. Endotoxin-responsive sequences control cachectin/tumor necrosis factor biosynthesis at the translational level. J. Exp. Med. 171, 465–475 (1990).

    Article  CAS  PubMed  Google Scholar 

  21. Chen, Y.L. et al. Differential regulation of ARE-mediated TNFα and IL-1β mRNA stability by lipopolysaccharide in RAW264.7 cells. Biochem. Biophys. Res. Commun. 346, 160–168 (2006).

    Article  CAS  PubMed  Google Scholar 

  22. Werner, S.L., Barken, D. & Hoffmann, A. Stimulus specificity of gene expression programs determined by temporal control of IKK activity. Science 309, 1857–1861 (2005).

    Article  CAS  PubMed  Google Scholar 

  23. Covert, M.W., Leung, T.H., Gaston, J.E. & Baltimore, D. Achieving stability of lipopolysaccharide-induced NF-κB activation. Science 309, 1854–1857 (2005).

    Article  CAS  PubMed  Google Scholar 

  24. Doyle, S. et al. IRF3 mediates a TLR3/TLR4-specific antiviral gene program. Immunity 17, 251–263 (2002).

    Article  CAS  PubMed  Google Scholar 

  25. Beutler, B., Krochin, N., Milsark, I.W., Luedke, C. & Cerami, A. Control of cachectin (tumor necrosis factor) synthesis: mechanisms of endotoxin resistance. Science 232, 977–980 (1986).

    Article  CAS  PubMed  Google Scholar 

  26. Caput, D. et al. Identification of a common nucleotide sequence in the 3′-untranslated region of mRNA molecules specifying inflammatory mediators. Proc. Natl. Acad. Sci. USA 83, 1670–1674 (1986).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Zubiaga, A.M., Belasco, J.G. & Greenberg, M.E. The nonamer UUAUUUAUU is the key AU-rich sequence motif that mediates mRNA degradation. Mol. Cell. Biol. 15, 2219–2230 (1995).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Barreau, C., Paillard, L. & Osborne, H.B. AU-rich elements and associated factors: are there unifying principles? Nucleic Acids Res. 33, 7138–7150 (2005).

    Article  CAS  PubMed  Google Scholar 

  29. Leung, T.H., Hoffmann, A. & Baltimore, D. One nucleotide in a κB site can determine cofactor specificity for NF-κB dimers. Cell 118, 453–464 (2004).

    Article  CAS  PubMed  Google Scholar 

  30. Hoffmann, A., Levchenko, A., Scott, M.L. & Baltimore, D. The IκB-NF-κB signaling module: temporal control and selective gene activation. Science 298, 1241–1245 (2002).

    Article  CAS  PubMed  Google Scholar 

  31. DiDonato, J.A., Hayakawa, M., Rothwarf, D.M., Zandi, E. & Karin, M. A cytokine-responsive IκB kinase that activates the transcription factor NF-κB. Nature 388, 548–554 (1997).

    Article  CAS  PubMed  Google Scholar 

  32. Lee, E.G. et al. Failure to regulate TNF-induced NF-κB and cell death responses in A20-deficient mice. Science 289, 2350–2354 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Beg, A.A., Finco, T.S., Nantermet, P.V. & Baldwin, A.S., Jr. Tumor necrosis factor and interleukin-1 lead to phosphorylation and loss of IκBα: a mechanism for NF-κB activation. Mol. Cell. Biol. 13, 3301–3310 (1993).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Sun, S.C., Ganchi, P.A., Ballard, D.W. & Greene, W.C. NF-kappa B controls expression of inhibitor IκBα: evidence for an inducible autoregulatory pathway. Science 259, 1912–1915 (1993).

    Article  CAS  PubMed  Google Scholar 

  35. Yarilina, A., Park-Min, K.H., Antoniv, T., Hu, X. & Ivashkiv, L.B. TNF activates an IRF1-dependent autocrine loop leading to sustained expression of chemokines and STAT1-dependent type I interferon-response genes. Nat. Immunol. 9, 378–387 (2008).

    Article  CAS  PubMed  Google Scholar 

  36. Tullai, J.W. et al. Immediate-early and delayed primary response genes are distinct in function and genomic architecture. J. Biol. Chem. 282, 23981–23995 (2007).

    Article  CAS  PubMed  Google Scholar 

  37. Iyer, V.R. et al. The transcriptional program in the response of human fibroblasts to serum. Science 283, 83–87 (1999).

    Article  CAS  PubMed  Google Scholar 

  38. Gilchrist, M. et al. Systems biology approaches identify ATF3 as a negative regulator of Toll-like receptor 4. Nature 441, 173–178 (2006).

    Article  CAS  PubMed  Google Scholar 

  39. Miller, A.D., Curran, T. & Verma, I.M. c-fos protein can induce cellular transformation: a novel mechanism of activation of a cellular oncogene. Cell 36, 51–60 (1984).

    Article  CAS  PubMed  Google Scholar 

  40. Lee, W.M., Lin, C. & Curran, T. Activation of the transforming potential of the human fos proto-oncogene requires message stabilization and results in increased amounts of partially modified fos protein. Mol. Cell. Biol. 8, 5521–5527 (1988).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Rollins, B.J. JE/MCP-1: an early-response gene encodes a monocyte-specific cytokine. Cancer Cells 3, 517–524 (1991).

    CAS  PubMed  Google Scholar 

  42. Van Damme, J., Proost, P., Lenaerts, J.P. & Opdenakker, G. Structural and functional identification of two human, tumor-derived monocyte chemotactic proteins (MCP-2 and MCP-3) belonging to the chemokine family. J. Exp. Med. 176, 59–65 (1992).

    Article  CAS  PubMed  Google Scholar 

  43. Neish, A.S., Williams, A.J., Palmer, H.J., Whitley, M.Z. & Collins, T. Functional analysis of the human vascular cell adhesion molecule 1 promoter. J. Exp. Med. 176, 1583–1593 (1992).

    Article  CAS  PubMed  Google Scholar 

  44. Becker, S., Warren, M.K. & Haskill, S. Colony-stimulating factor-induced monocyte survival and differentiation into macrophages in serum-free cultures. J. Immunol. 139, 3703–3709 (1987).

    CAS  PubMed  Google Scholar 

  45. Sarojini, H. et al. PEDF from mouse mesenchymal stem cell secretome attracts fibroblasts. J. Cell. Biochem. 104, 1793–1802 (2008).

    Article  CAS  PubMed  Google Scholar 

  46. Kong, W., Li, S., Longaker, M.T. & Lorenz, H.P. Cyclophilin C-associated protein is up-regulated during wound healing. J. Cell. Physiol. 210, 153–160 (2007).

    Article  CAS  PubMed  Google Scholar 

  47. McQuibban, G.A. et al. Matrix metalloproteinase processing of monocyte chemoattractant proteins generates CC chemokine receptor antagonists with anti-inflammatory properties in vivo. Blood 100, 1160–1167 (2002).

    CAS  PubMed  Google Scholar 

  48. McQuibban, G.A. et al. Inflammation dampened by gelatinase A cleavage of monocyte chemoattractant protein-3. Science 289, 1202–1206 (2000).

    Article  CAS  PubMed  Google Scholar 

  49. Dieu, M.C. et al. Selective recruitment of immature and mature dendritic cells by distinct chemokines expressed in different anatomic sites. J. Exp. Med. 188, 373–386 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Schmitz, J. et al. IL-33, an interleukin-1-like cytokine that signals via the IL-1 receptor-related protein ST2 and induces T helper type 2-associated cytokines. Immunity 23, 479–490 (2005).

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

We thank M. Boldin, R. O'Connell, X. Luo and K. Taganov for comments on the manuscript, and A. Balazs (California Institute of Technology) for the plasmid pHAGE2-CMV-eGFP-W. Supported by the National Institutes of Health (2R01GM039458 to D.B.) and the Millard and Muriel Jacobs Genetics and Genomics Laboratory at California Institute of Technology (microarray analysis).

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S.H. designed, did and analyzed the experiments; S.H. and D.B. wrote the manuscript.

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Correspondence to David Baltimore.

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Hao, S., Baltimore, D. The stability of mRNA influences the temporal order of the induction of genes encoding inflammatory molecules. Nat Immunol 10, 281–288 (2009). https://doi.org/10.1038/ni.1699

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