Ye, F., Lei, X. & Gao, S. J. Mechanisms of Kaposi’s sarcoma-associated herpesvirus latency and reactivation. Adv. Virol. 2011, 193860 (2011).
Desrosiers, R., Friderici, K. & Rottman, F. Identification of methylated nucleosides in messenger RNA from Novikoff hepatoma cells. Proc. Natl Acad. Sci. USA 71, 3971–3975 (1974).
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).
Linder, B. et al. Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome. Nat. Meth. 12, 767–772 (2015).
Bokar, J. A., Rath-Shambaugh, M. E., Ludwiczak, R., Narayan, P. & Rottman, F. Characterization and partial purification of mRNA N6-adenosine methyltransferase from HeLa cell nuclei. Internal mRNA methylation requires a multisubunit complex. J. Biol. Chem. 269, 17697–17704 (1994).
Bokar, J. A., Shambaugh, M. E., Polayes, D., Matera, A. G. & Rottman, F. M. Purification and cDNA cloning of the AdoMet-binding subunit of the human mRNA (N6-adenosine)-methyltransferase. RNA 3, 1233–1247 (1997).
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).
Ping, X. L. et al. Mammalian WTAP is a regulatory subunit of the RNA N6-methyladenosine methyltransferase. Cell Res. 24, 177–189 (2014).
Liu, J. et al. A METTL3-METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation. Nat. Chem. Biol. 10, 93–95 (2014).
Patil, D. P. et al. m6A RNA methylation promotes XIST-mediated transcriptional repression. Nature 537, 369–373 (2016).
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).
Zheng, G. et al. ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility. Mol. Cell 49, 18–29 (2013).
Mauer, J. et al. Reversible methylation of m6Am in the 5′ cap controls mRNA stability. Nature 541, 371–375 (2017).
Liu, N. et al. N6-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions. Nature 518, 560–564 (2015).
Zhou, K. I. et al. N6-methyladenosine modification in a long noncoding RNA hairpin predisposes Its conformation to protein binding. J. Mol. Biol. 428, 822–833 (2016).
Konig, J. et al. iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat. Struct. Mol. Biol. 17, 909–915 (2010).
Alarcon, C. R. et al. HNRNPA2B1 is a mediator of m6A-dependent nuclear RNA processing events. Cell 162, 1299–1308 (2015).
Wang, X. et al. N6-methyladenosine modulates messenger RNA translation efficiency. Cell 161, 1388–1399 (2015).
Wang, X. et al. N6-methyladenosine-dependent regulation of messenger RNA stability. Nature 505, 117–120 (2014).
Du, H. et al. YTHDF2 destabilizes m6A-containing RNA through direct recruitment of the CCR4-NOT deadenylase complex. Nat. Commun. 7, 12626 (2016).
Kennedy, E. M. et al. Posttranscriptional m6A Editing of HIV-1 mRNAs Enhances Viral Gene Expression. Cell Host Microbe 19, 675–685 (2016).
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).
Xiao, W. et al. Nuclear m6A reader YTHDC1 regulates mRNA splicing. Mol. Cell 61, 507–519 (2016).
Hsu, P. J. et al. Ythdc2 is an N6-methyladenosine binding protein that regulates mammalian spermatogenesis. Cell Res. 27, 1115–1127 (2017).
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).
Gokhale, N. S. et al. N6-Methyladenosine in Flaviviridae Viral RNA genomes regulates infection. Cell Host Microbe 20, 654–665 (2016).
Lichinchi, G. et al. Dynamics of human and viral RNA methylation during Zika virus infection. Cell Host Microbe 20, 666–673 (2016).
Tirumuru, N. et al. N6-methyladenosine of HIV-1 RNA regulates viral infection and HIV-1 Gag protein expression. eLife 5, e15528 (2016).
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).
Zhou, F. C. et al. Efficient infection by a recombinant Kaposi’s sarcoma-associated herpesvirus cloned in a bacterial artificial chromosome: application for genetic analysis. J. Virol. 76, 6185–6196 (2002).
Meng, J., Cui, X., Rao, M. K., Chen, Y. & Huang, Y. Exome-based analysis for RNA epigenome sequencing data. Bioinformatics 29, 1565–1567 (2013).
Brulois, K. F. et al. Construction and manipulation of a new Kaposi’s sarcoma-associated herpesvirus bacterial artificial chromosome clone. J. Virol. 86, 9708–9720 (2012).
Nakamura, H. et al. Global changes in Kaposi’s sarcoma-associated virus gene expression patterns following expression of a tetracycline-inducible Rta transactivator. J. Virol. 77, 4205–4220 (2003).
Jones, T. et al. Direct and efficient cellular transformation of primary rat mesenchymal precursor cells by KSHV. J. Clin. Invest. 122, 1076–1081 (2012).
Lee, M. S. et al. Human mesenchymal stem cells of diverse origins support persistent infection with Kaposi’s sarcoma-associated herpesvirus and manifest distinct angiogenic, invasive, and transforming phenotypes. mBio 7, e02109–15 (2016).
Xie, J., Ajibade, A. O., Ye, F., Kuhne, K. & Gao, S. J. Reactivation of Kaposi’s sarcoma-associated herpesvirus from latency requires MEK/ERK, JNK and p38 multiple mitogen-activated protein kinase pathways. Virology 371, 139–154 (2008).
Greene, W. & Gao, S. J. Actin dynamics regulate multiple endosomal steps during Kaposi’s sarcoma-associated herpesvirus entry and trafficking in endothelial cells. PLoS Pathog. 5, e1000512 (2009).
Davis, D. A. et al. Hypoxia induces lytic replication of Kaposi’s sarcoma-associated herpesvirus. Blood 97, 3244–3250 (2001).
Hollingworth, R. et al. Activation of DNA damage response pathways during lytic replication of KSHV. Viruses 7, 2908–2927 (2015).
Meyer, K. D. & Jaffrey, S. R. Rethinking m6A readers, writers, and erasers. Annu. Rev. Cell Dev. Biol. 33, 319–342 (2017).
Moss, B., Gershowitz, A., Stringer, J. R., Holland, L. E. & Wagner, E. K. 5′-Terminal and internal methylated nucleosides in herpes simplex virus type 1 mRNA. J. Virol. 23, 234–239 (1977).
Covarrubias, S. et al. Coordinated destruction of cellular messages in translation complexes by the gammaherpesvirus host shutoff factor and the mammalian exonuclease Xrn1. PLoS Pathog. 7, e1002339 (2011).
Chandriani, S. & Ganem, D. Host transcript accumulation during lytic KSHV infection reveals several classes of host responses. PLoS ONE 2, e811 (2007).
Chen, T., You, Y., Jiang, H. & Wang, Z. Z. Epithelial-mesenchymal transition (EMT): a biological process in the development, stem cell differentiation, and tumorigenesis. J. Cell Physiol. 232, 3261–3272 (2017).
Moustakas, A. & Heldin, C. H. Signaling networks guiding epithelial-mesenchymal transitions during embryogenesis and cancer progression. Cancer Sci. 98, 1512–1520 (2007).
Meyer, K. D. et al. 5′ UTR m6A promotes cap-independent translation. Cell 163, 999–1010 (2015).
Moody, R. et al. KSHV microRNAs mediate cellular transformation and tumorigenesis by redundantly targeting cell growth and survival pathways. PLoS Pathog. 9, e1003857 (2013).
Brulois, K. & Jung, J. U. Interplay between Kaposi’s sarcoma-associated herpesvirus and the innate immune system. Cytokine Growth Factor Rev. 25, 597–609 (2014).
Lee, M. S. et al. Exploitation of the complement system by oncogenic Kaposi’s sarcoma-associated herpesvirus for cell survival and persistent infection. PLoS Pathog. 10, e1004412 (2014).
Cheng, F. et al. Screening of the human kinome identifies MSK1/2-CREB1 as an essential pathway mediating Kaposi’s sarcoma-associated herpesvirus lytic replication during primary infection. J. Virol. 89, 9262–9280 (2015).
Gao, S. J., Deng, J. H. & Zhou, F. C. Productive lytic replication of a recombinant Kaposi’s sarcoma-associated herpesvirus in efficient primary infection of primary human endothelial cells. J. Virol. 77, 9738–9749 (2003).
Dominissini, D., Moshitch-Moshkovitz, S., Salmon-Divon, M., Amariglio, N. & Rechavi, G. Transcriptome-wide mapping of N6-methyladenosine by m6A-seq based on immunocapturing and massively parallel sequencing. Nat. Protoc. 8, 176–189 (2013).
Arias, C. et al. KSHV 2.0: a comprehensive annotation of the Kaposi’s sarcoma-associated herpesvirus genome using next-generation sequencing reveals novel genomic and functional features. PLoS Pathog. 10, e1003847 (2014).
Bai, Z. et al. Genomewide mapping and screening of Kaposi’s sarcoma-associated herpesvirus (KSHV) 3′ untranslated regions identify bicistronic and polycistronic viral transcripts as frequent targets of KSHV microRNAs. J. Virol. 88, 377–392 (2014).
Majerciak, V. et al. A viral genome landscape of RNA polyadenylation from KSHV latent to lytic infection. PLoS Pathog. 9, e1003749 (2013).
Pearce, M., Matsumura, S. & Wilson, A. C. Transcripts encoding K12, v-FLIP, v-cyclin, and the microRNA cluster of Kaposi’s sarcoma-associated herpesvirus originate from a common promoter. J. Virol. 79, 14457–14464 (2005).
Tang, S. & Zheng, Z. M. Kaposi’s sarcoma-associated herpesvirus K8 exon 3 contains three 5′-splice sites and harbors a K8.1 transcription start site. J. Biol. Chem. 277, 14547–14556 (2002).
Yamanegi, K., Tang, S. & Zheng, Z. M. Kaposi’s sarcoma-associated herpesvirus K8beta is derived from a spliced intermediate of K8 pre-mRNA and antagonizes K8alpha (K-bZIP) to induce p21 and p53 and blocks K8alpha-CDK2 interaction. J. Virol. 79, 14207–14221 (2005).
Kim, D. et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36 (2013).
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Meth. 9, 357–359 (2012).
Meng, J. et al. A protocol for RNA methylation differential analysis with MeRIP-Seq data and exomePeak R/Bioconductor package. Methods 69, 274–281 (2014).
Krishnamoorthy, K. & Thomson, J. A more powerful test for comparing two Poisson means. J. Stat. Plan. Inf. 119, 23–35 (2004).
Cui, X. et al. Guitar: An R/Bioconductor package for gene annotation guided transcriptomic analysis of RNA-related genomic features. Biomed. Res. Int. 2016, 8367534 (2016).
Bailey, T. L. et al. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 37, W202–W208 (2009).
Trapnell, C. et al. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat. Biotechnol. 31, 46–53 (2013).
Trapnell, C. et al. Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511–515 (2010).