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Dynamics of the human and viral m6A RNA methylomes during HIV-1 infection of T cells

Nature Microbiology volume 1, Article number: 16011 (2016) Cite this article

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Abstract

N6-methyladenosine (m6A) is the most prevalent internal modification of eukaryotic mRNA. Very little is known of the function of m6A in the immune system or its role in host–pathogen interactions. Here, we investigate the topology, dynamics and bidirectional influences of the viral–host RNA methylomes during HIV-1 infection of human CD4 T cells. We show that viral infection triggers a massive increase in m6A in both host and viral mRNAs. In HIV-1 mRNA, we identified 14 methylation peaks in coding and noncoding regions, splicing junctions and splicing regulatory sequences. We also identified a set of 56 human gene transcripts that were uniquely methylated in HIV-1-infected T cells and were enriched for functions in viral gene expression. The functional relevance of m6A for viral replication was demonstrated by silencing of the m6A writer or the eraser enzymes, which decreased or increased HIV-1 replication, respectively. Furthermore, methylation of two conserved adenosines in the stem loop II region of HIV-1 Rev response element (RRE) RNA enhanced binding of HIV-1 Rev protein to the RRE in vivo and influenced nuclear export of RNA. Our results identify a new mechanism for the control of HIV-1 replication and its interaction with the host immune system.

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Figure 1: m6A RNA methylation in T cells is promoted by HIV-1 infection and modulates viral replication.
Figure 2: RNA methylation profiles of HIV-1 and HIV-1-infected T cells.
Figure 3: m6A methylation modulates the interaction between Rev protein and RRE RNA.
Figure 4: HIV-1 replication and RNA nuclear export are perturbed by methylation of A7883 in the RRE bulge region.
Figure 5: Proposed model for modulation of the m6A modification in RRE RNA and its effect on HIV-1 replication.

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Acknowledgements

The authors thank S. Head and the staff of the Next Generation Sequencing core facility at the Scripps Research Institute for help with the early phase of the project and HT-seq. The authors thank J. Klabis for help with the preparation of figures, and members of the Rana laboratory for discussions and advice, especially T.-C. Chao and K. Chang. The authors thank the Sloan Foundation (2015-13964), the Bert L. and N. Kuggie Vallee Foundation, the Irma T. Hirschl and Monique Weill-Caulier Charitable Trusts, the WorldQuant Foundation and the STARR Consortium (I7-A765, I9-A9-071) and acknowledge support from the National Institutes of Health (EB020393, NS076465, C.E.M.; NIAID and NIDA AI43198, DA039562 and DA030199, T.M.R.).

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Authors and Affiliations

  1. Department of Pediatrics, University of California, San Diego School of Medicine, La Jolla, 92093, California, USA

    Gianluigi Lichinchi, Shang Gao, Vikas Bansal & Tariq M. Rana

  2. Program for RNA Biology and Graduate School of Biomedical Sciences, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, 92037, California, USA

    Gianluigi Lichinchi & Tariq M. Rana

  3. Department of Physiology and Biophysics and the Institute for Computational Biomedicine, Weill Cornell Medical College of Cornell University, 1305 York Avenue, New York, 10021, New York, USA

    Yogesh Saletore & Christopher E. Mason

  4. Environmental Toxicology Graduate Program and Department of Chemistry, University of California, Riverside, 92521, California, USA

    Gwendolyn Michelle Gonzalez & Yinsheng Wang

  5. The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, The Feil Family Brain and Mind Research Institute (BMRI), New York, 10021, New York, USA

    Christopher E. Mason

  6. Institute for Genomic Medicine and Moores Cancer Center, University of California San Diego, La Jolla, 92093, California, USA

    Tariq M. Rana

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  1. Gianluigi Lichinchi
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Contributions

G.L. designed and performed experiments, analysed data and wrote the paper. S.G. performed experiments and analysed data. Y.S. performed experiments and analysed data. G.M.G. performed experiments and analysed data. V.B., Y.W. and C.M. analysed data. T.M.R. contributed to the concept and design, data analysis and manuscript writing.

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Correspondence to Tariq M. Rana.

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Lichinchi, G., Gao, S., Saletore, Y. et al. Dynamics of the human and viral m6A RNA methylomes during HIV-1 infection of T cells. Nat Microbiol 1, 16011 (2016). https://doi.org/10.1038/nmicrobiol.2016.11

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