Dominissini, D. et al. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature 485, 201–206 (2012).
Meyer, K. D. et al. Comprehensive analysis of mRNA methylation reveals enrichment in 3′ UTRs and near stop codons. Cell 149, 1635–1646 (2012).
Ke, S. et al. m6A mRNA modifications are deposited in nascent pre-mRNA and are not required for splicing but do specify cytoplasmic turnover. Genes Dev. 31, 990–1006 (2017).
Wang, X. et al. N6-methyladenosine-dependent regulation of messenger RNA stability. Nature 505, 117–120 (2014).
Wang, X. et al. N(6)-methyladenosine modulates messenger RNA translation efficiency. Cell 161, 1388–1399 (2015).
Xiao, W. et al. Nuclear m6A reader YTHDC1 regulates mRNA splicing. Mol. Cell 61, 507–519 (2016).
Du, H. et al. YTHDF2 destabilizes m6A-containing RNA through direct recruitment of the CCR4–NOT deadenylase complex. Nat. Commun. 7, 12626 (2016).
Meyer, K. D. & Jaffrey, S. R. Rethinking m6A readers, writers, and erasers. Annu. Rev. Cell Dev. Biol. 33, 319–342 (2017).
Liu, J. et al. A METTL3–METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation. Nat. Chem. Biol. 10, 93–95 (2014).
Zhao, B. S., Roundtree, I. A. & He, C. Post-transcriptional gene regulation by mRNA modifications. Nat. Rev. Mol. Cell Biol. 18, 31–42 (2017).
Roundtree, I. A., Evans, M. E., Pan, T. & He, C. Dynamic RNA modifications in gene expression regulation. Cell 169, 1187–1200 (2017).
Jia, G. et al. N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nat. Chem. Biol. 7, 885–887 (2011).
Mauer, J. et al. Reversible methylation of m6Am in the 5’ cap controls mRNA stability. Nature 541, 371–375 (2017).
Zheng, G. et al. ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility. Mol. Cell 49, 18–29 (2013).
Schwartz, S. et al. High-resolution mapping reveals a conserved, widespread, dynamic mRNA methylation program in yeast meiosis. Cell 155, 1409–1421 (2013).
Fustin, J.-M. et al. RNA-methylation-dependent RNA processing controls the speed of the circadian clock. Cell 155, 793–806 (2013).
Xiang, Y. et al. RNA m6A methylation regulates the ultraviolet-induced DNA damage response. Nature 543, 573–576 (2017).
Geula, S. et al. m6A mRNA methylation facilitates resolution of naïve pluripotency toward differentiation. Science 347, 1002–1006 (2015).
Lence, T. et al. m6A modulates neuronal functions and sex determination in Drosophila. Nature 540, 242–247 (2016).
Zhang, C. et al. m6A modulates haematopoietic stem and progenitor cell specification. Nature 549, 273–276 (2017).
Yoon, K.-J. et al. Temporal control of mammalian cortical neurogenesis by m6A methylation. Cell 171, 877–889.e17 (2017).
Li, H.-B. et al. m6A mRNA methylation controls T cell homeostasis by targeting the IL-7/STAT5/SOCS pathways. Nature 548, 338–342 (2017).
Tong, J. et al. m6A mRNA methylation sustains Treg suppressive functions. Cell Res. 28, 253–256 (2018).
Kennedy, E. M., Courtney, D. G., Tsai, K. & Cullen, B. R. Viral epitranscriptomics. J. Virol. 91, e02263–16 (2017).
Courtney, D. G. et al. Epitranscriptomic enhancement of influenza A virus gene expression and replication. Cell Host Microbe 22, 377–386.e5 (2017).
Gokhale, N. S. et al. N6-methyladenosine in flaviviridae viral RNA genomes regulates infection. Cell Host Microbe 20, 654–665 (2016).
Hesser, C., Karijolich, J., Dominissini, D., He, C. & Glaunsinger, B. A. N6-methyladenosine modification and the YTHDF2 reader protein play cell type specific roles in lytic viral gene expression during Kaposi’s sarcoma-associated herpesvirus infection. PLoS Pathog. 14, e1006995 (2018).
Kennedy, E. M. et al. Posttranscriptional m(6)A editing of HIV-1 mRNAs enhances viral gene expression. Cell Host Microbe 19, 675–685 (2016).
Lichinchi, G. et al. Dynamics of human and viral RNA methylation during Zika virus infection. Cell Host Microbe 20, 666–673 (2016).
Lichinchi, G. et al. Dynamics of the human and viral m6A RNA methylomes during HIV-1 infection of T cells. Nat. Microbiol. 1, 16011 (2016).
Tan, B. et al. Viral and cellular N6-methyladenosine and N6,2’-O-dimethyladenosine epitranscriptomes in the KSHV life cycle. Nat. Microbiol. 3, 108–120 (2018).
Tirumuru, N. et al. N6-methyladenosine of HIV-1 RNA regulates viral infection and HIV-1 Gag protein expression. eLife 5, e15528 (2016).
Tsai, K., Courtney, D. G. & Cullen, B. R. Addition of m6A to SV40 late mRNAs enhances viral structural gene expression and replication. PLoS Pathog. 14, e1006919 (2018).
Ye, F., Chen, E. R. & Nilsen, T. W. Kaposi’s sarcoma-associated herpesvirus utilizes and manipulates RNA N6-adenosine methylation to promote lytic replication. J. Virol. 91, e00466–17 (2017).
Tirosh, O. et al. The transcription and translation landscapes during human cytomegalovirus infection reveal novel host–pathogen interactions. PLoS Pathog. 11, e1005288 (2015).
O’Connor, C. M., Vanicek, J. & Murphy, E. A. Host microRNA regulation of human cytomegalovirus immediate early protein translation promotes viral latency. J. Virol. 88, 5524–5532 (2014).
Lin, Q. et al. Enantioselective synthesis of Janus kinase inhibitor INCB018424 via an organocatalytic aza-Michael reaction. Org. Lett. 11, 1999–2002 (2009).
Karikó, K., Buckstein, M., Ni, H. & Weissman, D. Suppression of RNA recognition by Toll-like receptors: the impact of nucleoside modification and the evolutionary origin of RNA. Immunity 23, 165–175 (2005).
Durbin, A. F., Wang, C., Marcotrigiano, J. & Gehrke, L. RNAs containing modified nucleotides fail to trigger RIG-I conformational changes for innate immune signaling. mBio 7, e00833–16 (2016).
Ivashkiv, L. B. & Donlin, L. T. Regulation of type I interferon responses. Nat. Rev. Immunol. 14, 36–49 (2014).
Schoggins, J. W. & Rice, C. M. Interferon-stimulated genes and their antiviral effector functions. Curr. Opin. Virol. 1, 519–525 (2011).
Schwartz, S. et al. Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5’ sites. Cell Rep. 8, 284–296 (2014).
Fuchs, S. Y. Hope and fear for interferon: the receptor-centric outlook on the future of interferon therapy. J. Interf. Cytokine Res. 33, 211–225 (2013).
Yoshimura, A., Naka, T. & Kubo, M. SOCS proteins, cytokine signalling and immune regulation. Nat. Rev. Immunol. 7, 454–465 (2007).
Sarasin-Filipowicz, M. et al. Alpha interferon induces long-lasting refractoriness of JAK–STAT signaling in the mouse liver through induction of USP18/UBP43. Mol. Cell. Biol. 29, 4841–4851 (2009).
Gracias, D. T. et al. The microRNA miR-155 controls CD8+ T cell responses by regulating interferon signaling. Nat. Immunol. 14, 593–602 (2013).
Versteeg, G. A. & García-Sastre, A. Viral tricks to grid-lock the type I interferon system. Curr. Opin. Microbiol. 13, 508–516 (2010).
Zheng, Q., Hou, J., Zhou, Y., Li, Z. & Cao, X. The RNA helicase DDX46 inhibits innate immunity by entrapping m6A-demethylated antiviral transcripts in the nucleus. Nat. Immunol. 18, 1094–1103 (2017).
Shi, H. et al. YTHDF3 facilitates translation and decay of N6-methyladenosine-modified RNA. Cell Res. 27, 315–328 (2017).
Li, A. et al. Cytoplasmic m6A reader YTHDF3 promotes mRNA translation. Cell Res. 27, 444–447 (2017).
Achdout, H. et al. Enhanced recognition of human NK receptors after influenza virus infection. J. Immunol. 171, 915–923 (2003).
Wang, X. et al. Murine cytomegalovirus abortively infects human dendritic cells, leading to expression and presentation of virally vectored genes. J. Virol. 77, 7182–7192 (2003).
Meningher, T. et al. Relationships between A(H1N1)pdm09 influenza infection and infections with other respiratory viruses. Influenza Other Respir. Viruses 8, 422–430 (2014).
Sanjana, N. E., Shalem, O. & Zhang, F. Improved vectors and genome-wide libraries for CRISPR screening. Nat. Methods 11, 783–784 (2014).
Straussman, R. et al. Tumour micro-environment elicits innate resistance to RAF inhibitors through HGF secretion. Nature 487, 500–504 (2012).
McCarthy, D. J., Chen, Y. & Smyth, G. K. Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Res. 40, 4288–4297 (2012).
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
Cong, L. et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819–823 (2013).