Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Review Article
  • Published:

Interactions of NF-κB with chromatin: the art of being at the right place at the right time

Abstract

Transcription factors of the NF-κB family are essential regulators of the inflammatory and immune responses. The main 'switch' in NF-κB activation is cytoplasmic and leads to the release of NF-κB proteins from IκB molecules, specific inhibitors that prevent their nuclear accumulation. However, it is becoming increasingly apparent that in addition to this required activation step, both recruitment of NF-κB to target genes and NF-κB-induced transcriptional events after recruitment are actively controlled. Regulated recruitment of NF-κB to chromatin generates kinetic complexity in NF-κB-dependent gene induction and 'wires' NF-κB-regulated gene activity to simultaneously activated pathways and transcription factors.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Components of the NF-κB transcriptional system: Rel proteins, NF-κB dimers and κB sites.
Figure 2: Structural views of NF-κB and the nucleosome.
Figure 3: Regulatory 'layers' in NF-κB-dependent gene induction.

Similar content being viewed by others

References

  1. Verma, I.M., Stevenson, J.K., Schwarz, E.M., Van Antwerp, D. & Miyamoto, S. Rel/NF-κB/IκB family: intimate tales of association and dissociation. Genes Dev. 9, 2723–2735 (1995).

    Article  CAS  PubMed  Google Scholar 

  2. Baldwin, A.S., Jr. The NF-κB and IκB proteins: new discoveries and insights. Annu. Rev. Immunol. 14, 649–683 (1996).

    Article  CAS  PubMed  Google Scholar 

  3. Ghosh, S., May, M.J. & Kopp, E.B. NF-κB and Rel proteins: evolutionarily conserved mediators of immune responses. Annu. Rev. Immunol. 16, 225–260 (1998).

    Article  CAS  PubMed  Google Scholar 

  4. Liou, H.C., Sha, W.C., Scott, M.L. & Baltimore, D. Sequential induction of NF-κB/Rel family proteins during B-cell terminal differentiation. Mol. Cell. Biol. 14, 5349–5359 (1994).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Saccani, S., Pantano, S. & Natoli, G. Modulation of NF-κB activity by exchange of dimers. Mol. Cell 11, 1563–1574 (2003).

    Article  CAS  PubMed  Google Scholar 

  6. Grilli, M., Chiu, J.J. & Lenardo, M.J. NF-κB and Rel: participants in a multiform transcriptional regulatory system. Int. Rev. Cytol. 143, 1–62 (1993).

    Article  CAS  PubMed  Google Scholar 

  7. Verweij, C.L., Geerts, M. & Aarden, L.A. Activation of interleukin-2 gene transcription via the T-cell surface molecule CD28 is mediated through an NF-κB-like response element. J. Biol. Chem. 266, 14179–14182 (1991).

    CAS  PubMed  Google Scholar 

  8. Huang, D.B., Chen, Y.Q., Ruetsche, M., Phelps, C.B. & Ghosh, G. X-ray crystal structure of proto-oncogene product c-Rel bound to the CD28 response element of IL-2. Structure (Camb.) 9, 669–678 (2001).

    Article  CAS  Google Scholar 

  9. Hansen, S.K., Guerrini, L. & Blasi, F. Differential DNA sequence specificity and regulation of HIV-1 enhancer activity by cRel-RelA transcription factor. J. Biol. Chem. 269, 22230–22237 (1994).

    CAS  PubMed  Google Scholar 

  10. Martone, R. et al. Distribution of NF-κB-binding sites across human chromosome 22. Proc. Natl. Acad. Sci. USA 100, 12247–12252 (2003).

    Article  CAS  PubMed  Google Scholar 

  11. Hottiger, M.O., Felzien, L.K. & Nabel, G.J. Modulation of cytokine-induced HIV gene expression by competitive binding of transcription factors to the coactivator p300. EMBO J. 17, 3124–3134 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Cawley, S. et al. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116, 499–509 (2004).

    Article  CAS  PubMed  Google Scholar 

  13. Fernandez, P.C. et al. Genomic targets of the human c-Myc protein. Genes Dev. 17, 1115–1129 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Udalova, I.A., Mott, R., Field, D. & Kwiatkowski, D. Quantitative prediction of NF-κB DNA-protein interactions. Proc. Natl. Acad. Sci. USA 99, 8167–8172 (2002).

    Article  CAS  PubMed  Google Scholar 

  15. 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 

  16. Lin, R., Gewert, D. & Hiscott, J. Differential transcriptional activation in vitro by NF-κB/Rel proteins. J. Biol. Chem. 270, 3123–3131 (1995).

    Article  CAS  PubMed  Google Scholar 

  17. Algarte, M., Kwon, H., Genin, P. & Hiscott, J. Identification by in vivo genomic footprinting of a transcriptional switch containing NF-κB and Sp1 that regulates the IκBα promoter. Mol. Cell. Biol. 19, 6140–6153 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Bonizzi, G. et al. Activation of IKKα target genes depends on recognition of specific κB binding sites by RelB:p52 dimers. EMBO J. 23, 4202–4210 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Senftleben, U. et al. Activation by IKKα of a second, evolutionary conserved, NF-κB signaling pathway. Science 293, 1495–1499 (2001).

    Article  CAS  PubMed  Google Scholar 

  20. Govind, S. Control of development and immunity by rel transcription factors in Drosophila. Oncogene 18, 6875–6887 (1999).

    Article  CAS  PubMed  Google Scholar 

  21. Jiang, J. & Levine, M. Binding affinities and cooperative interactions with bHLH activators delimit threshold responses to the dorsal gradient morphogen. Cell 72, 741–752 (1993).

    Article  CAS  PubMed  Google Scholar 

  22. 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 

  23. Natoli, G. Little things that count in transcriptional regulation. Cell 118, 406–408 (2004).

    Article  CAS  PubMed  Google Scholar 

  24. Walker, S., Hayes, S. & O'Hare, P. Site-specific conformational alteration of the Oct-1 POU domain-DNA complex as the basis for differential recognition by Vmw65 (VP16). Cell 79, 841–852 (1994).

    Article  CAS  PubMed  Google Scholar 

  25. Lefstin, J.A. & Yamamoto, K.R. Allosteric effects of DNA on transcriptional regulators. Nature 392, 885–888 (1998).

    Article  CAS  PubMed  Google Scholar 

  26. Yamamoto, M. et al. Regulation of Toll/IL-1-receptor-mediated gene expression by the inducible nuclear protein IκBζ. Nature 430, 218–222 (2004).

    Article  CAS  PubMed  Google Scholar 

  27. Urban, M.B. & Baeuerle, P.A. The 65-kD subunit of NF-κB is a receptor for I κB and a modulator of DNA-binding specificity. Genes Dev. 4, 1975–1984 (1990).

    Article  CAS  PubMed  Google Scholar 

  28. Thanos, D. & Maniatis, T. Virus induction of human IFNβ gene expression requires the assembly of an enhanceosome. Cell 83, 1091–1100 (1995).

    Article  CAS  PubMed  Google Scholar 

  29. Chen-Park, F.E., Huang, D.B., Noro, B., Thanos, D. & Ghosh, G. The κB DNA sequence from the HIV long terminal repeat functions as an allosteric regulator of HIV transcription. J. Biol. Chem. 277, 24701–24708 (2002).

    Article  CAS  PubMed  Google Scholar 

  30. Saccani, S., Pantano, S. & Natoli, G. Two waves of nuclear factor κB recruitment to target promoters. J. Exp. Med. 193, 1351–1359 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Saccani, S., Marazzi, I., Beg, A.A. & Natoli, G. Degradation of promoter-bound p65/RelA is essential for the prompt termination of the nuclear factor κB response. J. Exp. Med. 200, 107–113 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Saccani, S., Pantano, S. & Natoli, G. p38-Dependent marking of inflammatory genes for increased NF-κB recruitment. Nat. Immunol. 3, 69–75 (2002).

    Article  CAS  PubMed  Google Scholar 

  33. Chen, D. et al. Regulation of transcription by a protein methyltransferase. Science 284, 2174–2177 (1999).

    Article  CAS  PubMed  Google Scholar 

  34. Covic, M. et al. Arginine methyltransferase CARM1 is a promoter-specific regulator of NF-κB-dependent gene expression. EMBO J. 24, 85–96 (2005).

    Article  CAS  PubMed  Google Scholar 

  35. Haller, D. et al. Transforming growth factor-β 1 inhibits non-pathogenic Gram negative bacteria-induced NF-κB recruitment to the interleukin-6 gene promoter in intestinal epithelial cells through modulation of histone acetylation. J. Biol. Chem. 278, 23851–23860 (2003).

    Article  CAS  PubMed  Google Scholar 

  36. Phelps, C.B., Sengchanthalangsy, L.L., Malek, S. & Ghosh, G. Mechanism of κB DNA binding by Rel/NF-κB dimers. J. Biol. Chem. 275, 24392–24399 (2000).

    Article  CAS  PubMed  Google Scholar 

  37. Munshi, N. et al. Coordination of a transcriptional switch by HMGI(Y) acetylation. Science 293, 1133–1136 (2001).

    Article  CAS  PubMed  Google Scholar 

  38. Genin, P., Algarte, M., Roof, P., Lin, R. & Hiscott, J. Regulation of RANTES chemokine gene expression requires cooperativity between NF-κB and IFN-regulatory factor transcription factors. J. Immunol. 164, 5352–5361 (2000).

    Article  CAS  PubMed  Google Scholar 

  39. Guo, Z., Boekhoudt, G.H. & Boss, J.M. Role of the intronic enhancer in tumor necrosis factor-mediated induction of manganous superoxide dismutase. J. Biol. Chem. 278, 23570–23578 (2003).

    Article  CAS  PubMed  Google Scholar 

  40. Boekhoudt, G.H., Guo, Z., Beresford, G.W. & Boss, J.M. Communication between NF-κB and Sp1 controls histone acetylation within the proximal promoter of the monocyte chemoattractant protein 1 gene. J. Immunol. 170, 4139–4147 (2003).

    Article  CAS  PubMed  Google Scholar 

  41. Kornberg, R.D. & Lorch, Y. Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell 98, 285–294 (1999).

    Article  CAS  PubMed  Google Scholar 

  42. Imbalzano, A.N., Kwon, H., Green, M.R. & Kingston, R.E. Facilitated binding of TATA-binding protein to nucleosomal DNA. Nature 370, 481–485 (1994).

    Article  CAS  PubMed  Google Scholar 

  43. Taylor, I.C., Workman, J.L., Schuetz, T.J. & Kingston, R.E. Facilitated binding of GAL4 and heat shock factor to nucleosomal templates: differential function of DNA-binding domains. Genes Dev. 5, 1285–1298 (1991).

    Article  CAS  PubMed  Google Scholar 

  44. Li, B., Adams, C.C. & Workman, J.L. Nucleosome binding by the constitutive transcription factor Sp1. J. Biol. Chem. 269, 7756–7763 (1994).

    CAS  PubMed  Google Scholar 

  45. Perlmann, T. & Wrange, O. Specific glucocorticoid receptor binding to DNA reconstituted in a nucleosome. EMBO J. 7, 3073–3079 (1988).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Anderson, J.D. & Widom, J. Sequence and position-dependence of the equilibrium accessibility of nucleosomal DNA target sites. J. Mol. Biol. 296, 979–987 (2000).

    Article  CAS  PubMed  Google Scholar 

  47. Polach, K.J. & Widom, J. Mechanism of protein access to specific DNA sequences in chromatin: a dynamic equilibrium model for gene regulation. J. Mol. Biol. 254, 130–149 (1995).

    Article  CAS  PubMed  Google Scholar 

  48. Widom, J. Structure, dynamics, and function of chromatin in vitro. Annu. Rev. Biophys. Biomol. Struct. 27, 285–327 (1998).

    Article  CAS  PubMed  Google Scholar 

  49. Li, Q. & Wrange, O. Accessibility of a glucocorticoid response element in a nucleosome depends on its rotational positioning. Mol. Cell. Biol. 15, 4375–4384 (1995).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Ghosh, G., van Duyne, G., Ghosh, S. & Sigler, P.B. Structure of NF-κB p50 homodimer bound to a κB site. Nature 373, 303–310 (1995).

    Article  CAS  PubMed  Google Scholar 

  51. Muller, C.W., Rey, F.A., Sodeoka, M., Verdine, G.L. & Harrison, S.C. Structure of the NF-κB p50 homodimer bound to DNA. Nature 373, 311–317 (1995).

    Article  CAS  PubMed  Google Scholar 

  52. Chen, F.E., Huang, D.B., Chen, Y.Q. & Ghosh, G. Crystal structure of p50/p65 heterodimer of transcription factor NF-κB bound to DNA. Nature 391, 410–413 (1998).

    Article  CAS  PubMed  Google Scholar 

  53. Huxford, T., Malek, S. & Ghosh, G. Structure and mechanism in NF-κB/IκB signaling. Cold Spring Harb. Symp. Quant. Biol. 64, 533–540 (1999).

    Article  CAS  PubMed  Google Scholar 

  54. Angelov, D. et al. The histone octamer is invisible when NF-κB binds to the nucleosome. J. Biol. Chem. 279, 42374–42382 (2004).

    Article  CAS  PubMed  Google Scholar 

  55. Steger, D.J. & Workman, J.L. Stable co-occupancy of transcription factors and histones at the HIV-1 enhancer. EMBO J. 16, 2463–2472 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Holloway, A.F., Rao, S., Chen, X. & Shannon, M.F. Changes in chromatin accessibility across the GM-CSF promoter upon T cell activation are dependent on nuclear factor κB proteins. J. Exp. Med. 197, 413–423 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Weinmann, A.S., Plevy, S.E. & Smale, S.T. Rapid and selective remodeling of a positioned nucleosome during the induction of IL-12 p40 transcription. Immunity 11, 665–675 (1999).

    Article  CAS  PubMed  Google Scholar 

  58. Agalioti, T. et al. Ordered recruitment of chromatin modifying and general transcription factors to the IFN-β promoter. Cell 103, 667–678 (2000).

    Article  CAS  PubMed  Google Scholar 

  59. Lomvardas, S. & Thanos, D. Nucleosome sliding via TBP DNA binding in vivo. Cell 106, 685–696 (2001).

    Article  CAS  PubMed  Google Scholar 

  60. Angelov, D. et al. The histone variant macroH2A interferes with transcription factor binding and SWI/SNF nucleosome remodeling. Mol. Cell 11, 1033–1041 (2003).

    Article  CAS  PubMed  Google Scholar 

  61. Perche, P.Y. et al. Higher concentrations of histone macroH2A in the Barr body are correlated with higher nucleosome density. Curr. Biol. 10, 1531–1534 (2000).

    Article  CAS  PubMed  Google Scholar 

  62. De Bosscher, K., Vanden Berghe, W. & Haegeman, G. The interplay between the glucocorticoid receptor and nuclear factor-κB or activator protein-1: molecular mechanisms for gene repression. Endocr. Rev. 24, 488–522 (2003).

    Article  CAS  PubMed  Google Scholar 

  63. Nissen, R.M. & Yamamoto, K.R. The glucocorticoid receptor inhibits NFκB by interfering with serine-2 phosphorylation of the RNA polymerase II carboxy-terminal domain. Genes Dev. 14, 2314–2329 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Price, D.H. P-TEFb, a cyclin-dependent kinase controlling elongation by RNA polymerase II. Mol. Cell. Biol. 20, 2629–2634 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Kassel, O. et al. A nuclear isoform of the focal adhesion LIM-domain protein Trip6 integrates activating and repressing signals at AP-1- and NF-κB-regulated promoters. Genes Dev. 18, 2518–2528 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Barboric, M., Nissen, R.M., Kanazawa, S., Jabrane-Ferrat, N. & Peterlin, B.M. NF-κB binds P-TEFb to stimulate transcriptional elongation by RNA polymerase II. Mol. Cell 8, 327–337 (2001).

    Article  CAS  PubMed  Google Scholar 

  67. Zhong, H., May, M.J., Jimi, E. & Ghosh, S. The phosphorylation status of nuclear NF-κB determines its association with CBP/p300 or HDAC-1. Mol. Cell 9, 625–636 (2002).

    Article  CAS  PubMed  Google Scholar 

  68. Duran, A., Diaz-Meco, M.T. & Moscat, J. Essential role of RelA Ser311 phosphorylation by ζPKC in NF-κB transcriptional activation. EMBO J. 22, 3910–3918 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Vermeulen, L., De Wilde, G., Van Damme, P., Vanden Berghe, W. & Haegeman, G. Transcriptional activation of the NF-κB p65 subunit by mitogen- and stress-activated protein kinase-1 (MSK1). EMBO J. 22, 1313–1324 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Anest, V. et al. A nucleosomal function for IκB kinase-α in NF-κB-dependent gene expression. Nature 423, 659–663 (2003).

    Article  CAS  PubMed  Google Scholar 

  71. Yamamoto, Y., Verma, U.N., Prajapati, S., Kwak, Y.T. & Gaynor, R.B. Histone H3 phosphorylation by IKK-α is critical for cytokine-induced gene expression. Nature 423, 655–659 (2003).

    Article  CAS  PubMed  Google Scholar 

  72. Hoberg, J.E., Yeung, F. & Mayo, M.W. SMRT derepression by the IκB kinase α: a prerequisite to NF-κB transcription and survival. Mol. Cell 16, 245–255 (2004).

    Article  CAS  PubMed  Google Scholar 

  73. Chen, L.F. & Greene, W.C. Shaping the nuclear action of NF-κB. Nat. Rev. Mol. Cell Biol. 5, 392–401 (2004).

    Article  CAS  PubMed  Google Scholar 

  74. Yamamoto, Y. & Gaynor, R.B. IκB kinases: key regulators of the NF-κB pathway. Trends Biochem. Sci. 29, 72–79 (2004).

    Article  CAS  PubMed  Google Scholar 

  75. Zabel, U. & Baeuerle, P.A. Purified human IκB can rapidly dissociate the complex of the NF-κB transcription factor with its cognate DNA. Cell 61, 255–265 (1990).

    Article  CAS  PubMed  Google Scholar 

  76. Arenzana-Seisdedos, F. et al. Inducible nuclear expression of newly synthesized IκBα negatively regulates DNA-binding and transcriptional activities of NF-κB. Mol. Cell. Biol. 15, 2689–2696 (1995).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Beg, A.A., Sha, W.C., Bronson, R.T. & Baltimore, D. Constitutive NF-κB activation, enhanced granulopoiesis, and neonatal lethality in IκBα-deficient mice. Genes Dev. 9, 2736–2746 (1995).

    Article  CAS  PubMed  Google Scholar 

  78. Arenzana-Seisdedos, F. et al. Nuclear localization of IκB alpha promotes active transport of NF-κB from the nucleus to the cytoplasm. J. Cell Sci. 110, 369–378 (1997).

    CAS  PubMed  Google Scholar 

  79. Kung, A.L. et al. Small molecule blockade of transcriptional coactivation of the hypoxia-inducible factor pathway. Cancer Cell 6, 33–43 (2004).

    Article  CAS  PubMed  Google Scholar 

  80. Lepourcelet, M. et al. Small-molecule antagonists of the oncogenic Tcf/β-catenin protein complex. Cancer Cell 5, 91–102 (2004).

    Article  CAS  PubMed  Google Scholar 

  81. Lenhard, B. et al. Identification of conserved regulatory elements by comparative genome analysis. J. Biol. 2, 13 (2003).

    Article  PubMed  PubMed Central  Google Scholar 

  82. Kunsch, C., Ruben, S.M. & Rosen, C.A. Selection of optimal κB/Rel DNA-binding motifs: interaction of both subunits of NF-κB with DNA is required for transcriptional activation. Mol. Cell. Biol. 12, 4412–4421 (1992).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Luger, K., Mader, A.W., Richmond, R.K., Sargent, D.F. & Richmond, T.J. Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389, 251–260 (1997).

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank S. Dimitrov (Institute Albert Bonniot, Grenoble, Switzerland) and M.E. Bianchi (Dipartimento Biotecnologie, San Raffaele Institute, Milan, Italy) for discussions and insights; and W. Vandenberghe and G. Haegeman (University of Gent, Gent, Belgium) for suggestions on the manuscript. Supported by the Swiss National Science Foundation and Swiss League against Cancer.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Gioacchino Natoli.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Natoli, G., Saccani, S., Bosisio, D. et al. Interactions of NF-κB with chromatin: the art of being at the right place at the right time. Nat Immunol 6, 439–445 (2005). https://doi.org/10.1038/ni1196

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/ni1196

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing