Abstract

Viral infection is commonly associated with virus-driven hijacking of host proteins. Here we describe a novel mechanism by which influenza virus affects host cells through the interaction of influenza non-structural protein 1 (NS1) with the infected cell epigenome. We show that the NS1 protein of influenza A H3N2 subtype possesses a histone-like sequence (histone mimic) that is used by the virus to target the human PAF1 transcription elongation complex (hPAF1C). We demonstrate that binding of NS1 to hPAF1C depends on the NS1 histone mimic and results in suppression of hPAF1C-mediated transcriptional elongation. Furthermore, human PAF1 has a crucial role in the antiviral response. Loss of hPAF1C binding by NS1 attenuates influenza infection, whereas hPAF1C deficiency reduces antiviral gene expression and renders cells more susceptible to viruses. We propose that the histone mimic in NS1 enables the influenza virus to affect inducible gene expression selectively, thus contributing to suppression of the antiviral response.

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Acknowledgements

We thank P. deGross and A. Rudensky for the mass spectroscopy analysis of the NS1 binding proteins. A. Rojas Soto, D. Reinberg, M. Dobenecker and T. Zhanyun provided us with recombinant CHD1 (A.R.S., D.R.), recombinant Set7/9 (M.D.) and Set1C (T.Z.). F. Casadio, P. Lewis, O. Binda, O. Gozani, N. Levenkova, A. Mele, R. Darnell, L. Core, J. Lis and P. Palese gave us valuable technical advice and help with data analysis. We acknowledge the Rockefeller University Genomics Resource Center for technical support. We thank R. Cadagan, A. Santana, W. Huang, R. Chandramouli and H. Zebronsky for technical assistance, R. Rizzo for help with manuscript preparation and C. Nathan for discussion. L.M.K. for artwork. B.M is supported by NIH/NIAID K99 Pathway to Independence award (1K99AI095320-01). A.G.-S. is partially supported by NIAID grants R01AI046954, U19AI083025 and by CRIP (Center for Research in Influenza Pathogenesis), an NIAID funded Center of Excellence for Influenza Research and Surveillance, HHSN266200700010C. R.G.R. is supported by NIH grant CA129325. J.K. is supported by Charles H. Revson Foundation. I.M. is supported by American Italian Cancer Foundation. J.H. is supported by the Agency for Science, Technology and Research (A*STAR), Singapore. A.T. is supported by the NIH grant R01AI068058 and by Starr Cancer Consortium.

Author information

Affiliations

  1. Laboratory of Immune Cell Epigenetics and Signaling, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA

    • Ivan Marazzi
    • , Jessica S. Y. Ho
    • , Uwe Schaefer
    • , Kate L. Jeffrey
    •  & Alexander Tarakhovsky
  2. Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA

    • Jaehoon Kim
    •  & Robert G. Roeder
  3. Department of Microbiology, Mount Sinai School of Medicine, One Gustave L. Levy Place, Box 1124, New York, New York 10029, USA

    • Balaji Manicassamy
    • , Randy A. Albrecht
    • , Chris W. Seibert
    •  & Adolfo García-Sastre
  4. Global Health and Infectious Pathogens Institute, Mount Sinai School of Medicine, One Gustave L. Levy Place, Box 1124, New York, New York 10029, USA

    • Balaji Manicassamy
    • , Randy A. Albrecht
    •  & Adolfo García-Sastre
  5. Genomics Resource Center, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA

    • Scott Dewell
  6. Epinova DPU, Immuno-Inflammation Centre of Excellence for Drug Discovery, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, UK

    • Rab K. Prinjha
    •  & Kevin Lee
  7. Department of Medicine, Division of Infectious Diseases, Mount Sinai School of Medicine, One Gustave L. Levy Place, Box 1124, New York, New York 10029, USA

    • Adolfo García-Sastre

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Contributions

I.M. contributed to design, execution, analysis of the experiments and manuscript preparation. J.S.Y.H. studied the role of PAF1 in viral infection and assisted in manuscript preparation. J.K. and R.R. studied the impact of NS1 on hPAF1C and transcriptional elongation. B.M., R.A.A. engineered the recombinant influenza viruses and studied viral infectivity. U.S. was involved in gene expression studies. S.D. performed bioinformatic analysis. C.W.S. generated antibody against viral polymerase. K.L.J. gave technical assistance. R.K.P. and K.L. contributed to manuscript preparation and enabled ChIP-seq and RNA-seq. A.G.-S. supervised and discussed the work with infectious influenza viruses. A.T. conceived and supervised this study and wrote the final manuscript.

Competing interests

R.K.P. and K.L. are employees of GlaxoSmithKline. Research support, excluding salaries to the members of The Rockefeller University, was partially provided by GlaxoSmithKline.

Corresponding authors

Correspondence to Ivan Marazzi or Alexander Tarakhovsky.

Supplementary information

PDF files

  1. 1.

    Supplementary Information

    This file contains Supplementary Figures 1-12, Supplementary Methods, additional references and full legends for Supplementary Tables 1-8.

Excel files

  1. 1.

    Supplementary Table 1

    This table shows genes affected by Influenza Infection - see Supplementary Information file for full legend.

  2. 2.

    Supplementary Table 2

    This table contains a list of genes used for the integrated ChIP-seq profile - see Supplementary Information file for full legend.

  3. 3.

    Supplementary Table 3

    This table shows siPAF dependent genes in PR8/∆NS1 infected cells - see Supplementary Information file for full legend.

  4. 4.

    Supplementary Table 4

    This table shows siPAF dependent genes in Influenza (H1N1) infected cells - see Supplementary Information file for full legend.

  5. 5.

    Supplementary Table 5

    This table shows siPAF dependent genes in Influenza (H1N1) infected cells - see Supplementary Information file for full legend.

  6. 6.

    Supplementary Table 6

    This table shows siPAF dependent genes in Poly(I:C) transfected cells - see Supplementary Information file for full legend.

  7. 7.

    Supplementary Table 7

    This table shows siPAF dependent genes in IFNβ1 treated cells - see Supplementary Information file for full legend.

  8. 8.

    Supplementary Table 8

    This table shows that expression of housekeeping genes are not affected by siPAF mediated hPAF1 deficiency - see Supplementary Information file for full legend.

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DOI

https://doi.org/10.1038/nature10892

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