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

References

  1. Sharp, P. A. The centrality of RNA. Cell 136, 577–580 (2009).
    Article Google Scholar
  2. Squires, J. E. et al. Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA. Nucleic Acids Res. 40, 5023–5033 (2012).
    Article Google Scholar
  3. Yi, C. & Pan, T. Cellular dynamics of RNA modification. Acc. Chem. Res. 44, 1380–1388 (2011).
    Article Google Scholar
  4. Desrosiers, R. C., Friderici, K. H. & Rottman, F. M. Characterization of Novikoff hepatoma mRNA methylation and heterogeneity in the methylated 5′ terminus. Biochemistry 14, 4367–4374 (1975).
    Article Google Scholar
  5. Perry, R. P., Kelley, D. E., Friderici, K. & Rottman, F. The methylated constituents of L cell messenger RNA: evidence for an unusual cluster at the 5′ terminus. Cell 4, 387–394 (1975).
    Article Google Scholar
  6. Schibler, U., Kelley, D. E. & Perry, R. P. Comparison of methylated sequences in messenger RNA and heterogeneous nuclear RNA from mouse L cells. J. Mol. Biol. 115, 695–714 (1977).
    Article Google Scholar
  7. Wei, C. M., Gershowitz, A. & Moss, B. Methylated nucleotides block 5′ terminus of HeLa cell messenger RNA. Cell 4, 379–386 (1975).
    Article Google Scholar
  8. Meyer, K. D. et al. Comprehensive analysis of mRNA methylation reveals enrichment in 3′ UTRs and near stop codons. Cell 149, 1635–1646 (2012).
    Article Google Scholar
  9. Dominissini, D. et al. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature 485, 201–206 (2012).
    Article Google Scholar
  10. 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).
    Article Google Scholar
  11. Frayling, T. M. et al. A common variant in the FTO gene is associated with body mass index and predisposes to childhood and adult obesity. Science 316, 889–894 (2007).
    Article Google Scholar
  12. Jia, G. et al. N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nature Chem. Biol. 7, 885–887 (2011).
    Article Google Scholar
  13. Zheng, G. et al. ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility. Mol. Cell 49, 18–29 (2013).
    Article Google Scholar
  14. 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).
    Google Scholar
  15. Ping, X. L. et al. Mammalian WTAP is a regulatory subunit of the RNA N6-methyladenosine methyltransferase. Cell Res. 24, 177–189 (2014).
    Article Google Scholar
  16. Liu, J. et al. A METTL3–METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation. Nature Chem. Biol. 10, 93–95 (2014).
    Article Google Scholar
  17. Jia, G., Fu, Y. & He, C. Reversible RNA adenosine methylation in biological regulation. Trends Genet. 29, 108–115 (2013).
    Article Google Scholar
  18. Lee, M., Kim, B. & Kim, V. N. Emerging roles of RNA modification: m6A and U-tail. Cell 158, 980–987 (2014).
    Article Google Scholar
  19. Wang, X. et al. N6-methyladenosine-dependent regulation of messenger RNA stability. Nature 505, 117–120 (2014).
    Article Google Scholar
  20. Xu, C. et al. Structural basis for selective binding of m6A RNA by the YTHDC1 YTH domain. Nature Chem. Biol. 10, 927–929 (2014).
    Article Google Scholar
  21. Geula, S. et al. m6A mRNA methylation facilitates resolution of naive pluripotency toward differentiation. Science 347, 1002–1006 (2015).
    Article Google Scholar
  22. Liu, N. et al. N6-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions. Nature 518, 560–564 (2015).
    Article Google Scholar
  23. Zhou, J. et al. Dynamic m6A mRNA methylation directs translational control of heat shock response. Nature 526, 591–594 (2015).
    Article Google Scholar
  24. Zhao, X. et al. FTO-dependent demethylation of N6-methyladenosine regulates mRNA splicing and is required for adipogenesis. Cell Res. 24, 1403–1419 (2014).
    Article Google Scholar
  25. Fustin, J. M. et al. RNA-methylation-dependent RNA processing controls the speed of the circadian clock. Cell 155, 793–806 (2013).
    Article Google Scholar
  26. Batista, P. J. et al. m6A RNA modification controls cell fate transition in mammalian embryonic stem cells. Cell Stem Cell 15, 707–719 (2014).
    Article Google Scholar
  27. Wang, Y. et al. N6-methyladenosine modification destabilizes developmental regulators in embryonic stem cells. Nature Cell Biol. 16, 191–198 (2014).
    Article Google Scholar
  28. Kane, S. E. & Beemon, K. Precise localization of m6A in Rous sarcoma virus RNA reveals clustering of methylation sites: implications for RNA processing. Mol. Cell. Biol. 5, 2298–2306 (1985).
    Article Google Scholar
  29. Krug, R. M., Morgan, M. A. & Shatkin, A. J. Influenza viral mRNA contains internal N6-methyladenosine and 5′-terminal 7-methylguanosine in cap structures. J. Virol. 20, 45–53 (1976).
    Google Scholar
  30. Finkel, D. & Groner, Y. Methylations of adenosine residues (m6A) in pre-mRNA are important for formation of late simian virus 40 mRNAs. Virology 131, 409–425 (1983).
    Article Google Scholar
  31. Fu, L. et al. Simultaneous quantification of methylated cytidine and adenosine in cellular and tissue RNA by nano-flow liquid chromatography–tandem mass spectrometry coupled with the stable isotope-dilution method. Anal. Chem. 87, 7653–7659 (2015).
    Article Google Scholar
  32. Heaphy, S. et al. HIV-1 regulator of virion expression (Rev) protein binds to an RNA stem-loop structure located within the Rev response element region. Cell 60, 685–693 (1990).
    Article Google Scholar
  33. Kjems, J., Brown, M., Chang, D. D. & Sharp, P. A. Structural analysis of the interaction between the human immunodeficiency virus Rev protein and the Rev response element. Proc. Natl Acad. Sci. USA 88, 683–687 (1991).
    Article Google Scholar
  34. Malim, M. H. et al. HIV-1 structural gene expression requires binding of the Rev trans-activator to its RNA target sequence. Cell 60, 675–683 (1990).
    Article Google Scholar
  35. Battiste, J. L. et al. Alpha helix-RNA major groove recognition in an HIV-1 rev peptide–RRE RNA complex. Science 273, 1547–1551 (1996).
    Article Google Scholar
  36. Harcourt, E. M., Ehrenschwender, T., Batista, P. J., Chang, H. Y. & Kool, E. T. Identification of a selective polymerase enables detection of N6-methyladenosine in RNA. J. Am. Chem. Soc. 135, 19079–19082 (2013).
    Article Google Scholar
  37. Heaphy, S., Finch, J. T., Gait, M. J., Karn, J. & Singh, M. Human immunodeficiency virus type 1 regulator of virion expression, rev, forms nucleoprotein filaments after binding to a purine-rich ‘bubble’ located within the rev-responsive region of viral mRNAs. Proc. Natl Acad. Sci. USA 88, 7366–7370 (1991).
    Article Google Scholar
  38. Tiley, L. S., Malim, M. H., Tewary, H. K., Stockley, P. G. & Cullen, B. R. Identification of a high-affinity RNA-binding site for the human immunodeficiency virus type 1 Rev protein. Proc. Natl Acad. Sci. USA 89, 758–762 (1992).
    Article Google Scholar
  39. Kjems, J., Calnan, B. J., Frankel, A. D. & Sharp, P. A. Specific binding of a basic peptide from HIV-1 Rev. EMBO J. 11, 1119–1129 (1992).
    Article Google Scholar
  40. Hammerschmid, M. et al. Scanning mutagenesis of the arginine-rich region of the human immunodeficiency virus type 1 Rev trans activator. J. Virol. 68, 7329–7335 (1994).
    Google Scholar
  41. Alarcon, C. R. et al. HNRNPA2B1 is a mediator of m6A-dependent nuclear RNA processing events. Cell 162, 1299–1308 (2015).
    Article Google Scholar
  42. Roost, C. et al. Structure and thermodynamics of N-methyladenosine in RNA: a spring-loaded base modification. J. Am. Chem. Soc. 137, 2107–2115 (2015).
    Article Google Scholar
  43. Spitale, R. C. et al. Structural imprints in vivo decode RNA regulatory mechanisms. Nature 519, 486–490 (2015).
    Article Google Scholar
  44. Saletore, Y. et al. The birth of the Epitranscriptome: deciphering the function of RNA modifications. Genome Biol. 13, 175 (2012).
    Article Google Scholar
  45. Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
    Article Google Scholar
  46. Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).
    Article Google Scholar
  47. Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139–140 (2010).
    Article Google Scholar
  48. Kalland, K. H., Szilvay, A. M., Langhoff, E. & Haukenes, G. Subcellular distribution of human immunodeficiency virus type 1 Rev and colocalization of Rev with RNA splicing factors in a speckled pattern in the nucleoplasm. J. Virol. 68, 1475–1485 (1994).
    Google Scholar

Download references