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Lysine methylation of the NF-κB subunit RelA by SETD6 couples activity of the histone methyltransferase GLP at chromatin to tonic repression of NF-κB signaling

Nature Immunology volume 12, pages 2936 (2011) | Download Citation

Abstract

Signaling via the methylation of lysine residues in proteins has been linked to diverse biological and disease processes, yet the catalytic activity and substrate specificity of many human protein lysine methyltransferases (PKMTs) are unknown. We screened over 40 candidate PKMTs and identified SETD6 as a methyltransferase that monomethylated chromatin-associated transcription factor NF-κB subunit RelA at Lys310 (RelAK310me1). SETD6-mediated methylation rendered RelA inert and attenuated RelA-driven transcriptional programs, including inflammatory responses in primary immune cells. RelAK310me1 was recognized by the ankryin repeat of the histone methyltransferase GLP, which under basal conditions promoted a repressed chromatin state at RelA target genes through GLP-mediated methylation of histone H3 Lys9 (H3K9). NF-κB-activation–linked phosphorylation of RelA at Ser311 by protein kinase C-ζ (PKC-ζ) blocked the binding of GLP to RelAK310me1 and relieved repression of the target gene. Our findings establish a previously uncharacterized mechanism by which chromatin signaling regulates inflammation programs.

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Acknowledgements

We thank R. Kingston and M. Simon (Harvard Medical School) for recombinant nucleosomes; J. Smith (University of Alabama Birmingham) for the PKC-ζ(ca) plasmid; W.C. Greene (University of California San Francisco) for RelA(1–431) cDNA and the κB-Luc luciferase reporter plasmid; D. Reinberg (New York University) for the NSD1(SET) plasmid; M. Covert (Stanford University) and T.D. Gilmore (Boston University) for the wild-type and Rela−/− mouse 3T3 cells; J. Moscat (University of Cincinnati College of Medicine) for the wild-type and Prkcz−/− MEFs; E. Engleman (Stanford University) for FL-B16 cells; E. Green for critical reading of the manuscript; and A. Alizadeh for comments. Supported by the National Institutes of Health (DA025800 to O.G. and M.T.B.; GM068680 to X.C.; and F32AI080086 to C.L.L.), the American Society for Mass Spectrometry (B.A.G.), the National Heart, Lung and Blood Institute (HHSN-268201999934C to P.J.U.), the National Institute of Allergy and Infectious Diseases (U19-AI082719 to P.J.U.), the Floren Family Trust (P.J.U.), the Genentech Foundation (A.J.K.), the European Molecular Biology Organization (D.L.), the Human Frontier Science Program (D.L.), the Machiah Foundation (D.L.), the Georgia Research Alliance (X.C.) and the Ellison Medical Foundation (O.G.)

Author information

Affiliations

  1. Department of Biology, Stanford University, Stanford, California, USA.

    • Dan Levy
    • , Alex J Kuo
    • , Peggie Cheung
    • , Chih Long Liu
    • , Andrew Y Kuo
    •  & Or Gozani
  2. Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA.

    • Yanqi Chang
    •  & Xiaodong Cheng
  3. Laboratory of Lymphocyte Signaling, The Rockefeller University, New York, New York, USA.

    • Uwe Schaefer
    •  & Alexander Tarakhovsky
  4. EpiNova DPU, Immuno-Inflammation group, GlaxoSmithKline, Stevenage, UK.

    • Christopher Kitson
    • , Rab K Prinjha
    •  & Kevin Lee
  5. Department of Carcinogenesis, M.D. Anderson Cancer Center, Smithville, Texas, USA.

    • Alexsandra Espejo
    •  & Mark T Bedford
  6. Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA.

    • Barry M Zee
    •  & Benjamin A Garcia
  7. Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, California, USA.

    • Chih Long Liu
    • , Stephanie Tangsombatvisit
    • , Regina Cheung
    •  & Paul J Utz
  8. Department of Endocrinology, Gerontology, and Metabolism Medicine, Stanford University School of Medicine, Stanford, California, USA.

    • Ruth I Tennen
    •  & Katrin F Chua
  9. Center for Cancer Epigenetics, University of Texas M.D. Anderson, Houston, Texas, USA.

    • Song Tanjing
    •  & Xiaobing Shi
  10. Geriatric Research, Education, and Clinical Center, VA Palo Alto Health Care System, Palo Alto, California, USA.

    • Katrin F Chua

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Contributions

D.L. did most of the molecular biology and cellular studies; Y.C. did binding affinity studies and modeling; A.J.K., P.C. and X.S. generated the PKMT library; A.J.K. identified and initially characterized the activity of SETD6 on RelA Lys310; B.Z. did mass spectrometry analysis; U.S. and C.K. did the primary cells experiments; A.E. did CADOR array experiments; C.L.L. analyzed gene expression data sets; R.I.T., S.T., A.Y.K., R.C. and S.T. provided technical support; X.S., P.J.U., K.C., B.G., R.P., M.B., A.T., X.C. and O.G. discussed studies; D.L. and O.G. designed studies, analyzed data, and wrote the paper; D.L. and A.J.K. contributed independently to the work; and all authors discussed and commented on the manuscript.

Competing interests

C.K., R.K.P. and K.L. are employees of GlaxoSmithKline.

Corresponding author

Correspondence to Or Gozani.

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DOI

https://doi.org/10.1038/ni.1968

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