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Noncoding RNA and its associated proteins as regulatory elements of the immune system

Abstract

The rapid changes in gene expression that accompany developmental transitions, stress responses and proliferation are controlled by signal-mediated coordination of transcriptional and post-transcriptional mechanisms. In recent years, understanding of the mechanics of these processes and the contexts in which they are employed during hematopoiesis and immune challenge has increased. An important aspect of this progress is recognition of the importance of RNA-binding proteins and noncoding RNAs. These have roles in the development and function of the immune system and in pathogen life cycles, and they represent an important aspect of intracellular immunity.

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Figure 1: Contribution of untranslated and coding sequence to the length of human interleukin mRNAs.
Figure 2: Diverse lncRNA mechanisms.
Figure 3: Processing in the nucleus regulates mRNA fate.
Figure 4: RNA and RBP interact to regulate gene expression.

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References

  1. Djebali, S. et al. Landscape of transcription in human cells. Nature 489, 101–108 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  2. Cech, T.R. & Steitz, J.A. The noncoding RNA revolution—trashing old rules to forge new ones. Cell 157, 77–94 (2014).

    CAS  PubMed  Google Scholar 

  3. Rinn, J.L. & Chang, H.Y. Genome regulation by long noncoding RNAs. Annu. Rev. Biochem. 81, 145–166 (2012).

    CAS  PubMed  Google Scholar 

  4. Chen, C.Y., Chen, S.T., Juan, H.F. & Huang, H.C. Lengthening of 3′ UTR increases with morphological complexity in animal evolution. Bioinformatics 28, 3178–3181 (2012).

    CAS  PubMed  Google Scholar 

  5. Carpenter, S. et al. A long noncoding RNA mediates both activation and repression of immune response genes. Science 341, 789–792 (2013).In this article, a lncRNA regulated by MyD88 and NF-kB is found to activate or suppress distinct classes of transcripts. The lncRNA interacts with an RBP known to regulate transcription.

    CAS  PubMed  PubMed Central  Google Scholar 

  6. Rapicavoli, N.A. et al. A mammalian pseudogene lncRNA at the interface of inflammation and anti-inflammatory therapeutics. eLife 2, e00762 (2013).

    PubMed  PubMed Central  Google Scholar 

  7. Hu, G. et al. Expression and regulation of intergenic long noncoding RNAs during T cell development and differentiation. Nat. Immunol. 14, 1190–1198 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  8. Geisler, S. & Coller, J. RNA in unexpected places: long noncoding RNA functions in diverse cellular contexts. Nat. Rev. Mol. Cell Biol. 14, 699–712 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Williams, G.T., Mourtada-Maarabouni, M. & Farzaneh, F. A critical role for noncoding RNA GAS5 in growth arrest and rapamycin inhibition in human T-lymphocytes. Biochem. Soc. Trans. 39, 482–486 (2011).

    CAS  PubMed  Google Scholar 

  10. Kino, T., Hurt, D.E., Ichijo, T., Nader, N. & Chrousos, G.P. Noncoding RNA Gas5 is a growth arrest- and starvation-associated repressor of the glucocorticoid receptor. Sci. Signal. 3, ra8 (2010).

    PubMed  PubMed Central  Google Scholar 

  11. Vigneau, S., Rohrlich, P.S., Brahic, M. & Bureau, J.F. Tmevpg1, a candidate gene for the control of Theiler's virus persistence, could be implicated in the regulation of gamma interferon. J. Virol. 77, 5632–5638 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  12. Gomez, J.A. et al. The NeST long ncRNA controls microbial susceptibility and epigenetic activation of the interferon-γ locus. Cell 152, 743–754 (2013).In this article, a noncoding RNA conferring resistance to salmonella is found to regulate histone methylation at the locus encoding IFN-γ. The lncRNA interacts with components of the methyltransferase.

    CAS  PubMed  PubMed Central  Google Scholar 

  13. Bentley, D.L. Coupling mRNA processing with transcription in time and space. Nat. Rev. Genet. 15, 163–175 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  14. Bhatt, D.M. et al. Transcript dynamics of proinflammatory genes revealed by sequence analysis of subcellular RNA fractions. Cell 150, 279–290 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Saletore, Y., Chen-Kiang, S. & Mason, C.E. Novel RNA regulatory mechanisms revealed in the epitranscriptome. RNA Biol. 10, 342–346 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  16. Schones, D.E. et al. Dynamic regulation of nucleosome positioning in the human genome. Cell 132, 887–898 (2008).

    CAS  PubMed  Google Scholar 

  17. Nagaike, T. & Manley, J.L. Transcriptional activators enhance polyadenylation of mRNA precursors. RNA Biol. 8, 964–967 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Takagaki, Y. & Manley, J.L. Levels of polyadenylation factor CstF-64 control IgM heavy chain mRNA accumulation and other events associated with B cell differentiation. Mol. Cell 2, 761–771 (1998).

    CAS  PubMed  Google Scholar 

  19. Martinez, N.M. & Lynch, K.W. Control of alternative splicing in immune responses: many regulators, many predictions, much still to learn. Immunol. Rev. 253, 216–236 (2013).

    PubMed  PubMed Central  Google Scholar 

  20. Weischenfeldt, J. et al. NMD is essential for hematopoietic stem and progenitor cells and for eliminating by-products of programmed DNA rearrangements. Genes Dev. 22, 1381–1396 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  21. Spellman, R., Llorian, M. & Smith, C.W. Crossregulation and functional redundancy between the splicing regulator PTB and its paralogs nPTB and ROD1. Mol. Cell 27, 420–434 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  22. Sandberg, R., Neilson, J.R., Sarma, A., Sharp, P.A. & Burge, C.B. Proliferating cells express mRNAs with shortened 3′ untranslated regions and fewer microRNA target sites. Science 320, 1643–1647 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  23. Lianoglou, S., Garg, V., Yang, J.L., Leslie, C.S. & Mayr, C. Ubiquitously transcribed genes use alternative polyadenylation to achieve tissue-specific expression. Genes Dev. 27, 2380–2396 (2013).This article presents an improved method for determining the site of polyadenylation applied to various cell types, including B lymphocytes.

    CAS  PubMed  PubMed Central  Google Scholar 

  24. Ameres, S.L. & Zamore, P.D. Diversifying microRNA sequence and function. Nat. Rev. Mol. Cell Biol. 14, 475–488 (2013).

    CAS  PubMed  Google Scholar 

  25. Wang, X. et al. N6-methyladenosine-dependent regulation of messenger RNA stability. Nature 505, 117–120 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  26. Sedger, L.M. microRNA control of interferons and interferon induced anti-viral activity. Mol. Immunol. 56, 781–793 (2013).

    CAS  PubMed  Google Scholar 

  27. Scott, D.D. & Norbury, C.J. RNA decay via 3′ uridylation. Biochim. Biophys. Acta 1829, 654–665 (2013).

    CAS  PubMed  Google Scholar 

  28. Wan, Y. et al. Landscape and variation of RNA secondary structure across the human transcriptome. Nature 505, 706–709 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  29. Rouskin, S., Zubradt, M., Washietl, S., Kellis, M. & Weissman, J.S. Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo. Nature 505, 701–705 (2014).

    CAS  PubMed  Google Scholar 

  30. Turner, M. & Hodson, D. Regulation of lymphocyte development and function by RNA-binding proteins. Curr. Opin. Immunol. 24, 160–165 (2012).

    CAS  PubMed  Google Scholar 

  31. Rabani, M. et al. Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells. Nat. Biotechnol. 29, 436–442 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  32. Friedel, C.C., Dolken, L., Ruzsics, Z., Koszinowski, U.H. & Zimmer, R. Conserved principles of mammalian transcriptional regulation revealed by RNA half-life. Nucleic Acids Res. 37, e115 (2009).

    PubMed  PubMed Central  Google Scholar 

  33. Turner, M. & Katsikis, P.D. A new mechanism of gene regulation mediated by noncoding RNA. J. Immunol. 189, 3–4 (2012).

    CAS  PubMed  Google Scholar 

  34. Kontoyiannis, D., Pasparakis, M., Pizarro, T.T., Cominelli, F. & Kollias, G. Impaired on/off regulation of TNF biosynthesis in mice lacking TNF AU-rich elements: implications for joint and gut-associated immunopathologies. Immunity 10, 387–398 (1999).

    CAS  PubMed  Google Scholar 

  35. Kedersha, N., Ivanov, P. & Anderson, P. Stress granules and cell signaling: more than just a passing phase? Trends Biochem. Sci. 38, 494–506 (2013).

    CAS  PubMed  Google Scholar 

  36. Ramachandran, S. & Palanisamy, V. Horizontal transfer of RNAs: exosomes as mediators of intercellular communication. Wiley Interdiscip. Rev. RNA 3, 286–293 (2012).

    CAS  PubMed  Google Scholar 

  37. Aucher, A., Rudnicka, D. & Davis, D.M. MicroRNAs transfer from human macrophages to hepato-carcinoma cells and inhibit proliferation. J. Immunol. 191, 6250–6260 (2013).

    CAS  PubMed  Google Scholar 

  38. Villarroya-Beltri, C. et al. Sumoylated hnRNPA2B1 controls the sorting of miRNAs into exosomes through binding to specific motifs. Nat. Comun. 4, 2980 (2013).This article provides an analysis of miRNA repertoire of T cell–secreted exosomes and offers important insights into the regulation of the nonrandom sorting of miRNA by RBPs.

    Google Scholar 

  39. Nolte-'t Hoen, E.N. et al. Deep sequencing of RNA from immune cell-derived vesicles uncovers the selective incorporation of small noncoding RNA biotypes with potential regulatory functions. Nucleic Acids Res. 40, 9272–9285 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  40. Huang, X. et al. Characterization of human plasma-derived exosomal RNAs by deep sequencing. BMC Genomics 14, 319 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  41. Ray, D. et al. A compendium of RNA-binding motifs for decoding gene regulation. Nature 499, 172–177 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  42. Leppek, K. et al. Roquin promotes constitutive mRNA decay via a conserved class of stem-loop recognition motifs. Cell 153, 869–881 (2013).In this article, a screen for proteins interacting with a sequence that promotes RNA decay from the TNF mRNA identifies roquin, an RBP previously linked to tolerance and follicular helper T cell function.

    CAS  PubMed  Google Scholar 

  43. Vinuesa, C.G. et al. A RING-type ubiquitin ligase family member required to repress follicular helper T cells and autoimmunity. Nature 435, 452–458 (2005).

    CAS  PubMed  Google Scholar 

  44. Vogel, K.U. et al. Roquin paralogs 1 and 2 redundantly repress the Icos and Ox40 costimulator mRNAs and control follicular helper T cell differentiation. Immunity 38, 655–668 (2013).

    CAS  PubMed  Google Scholar 

  45. Pratama, A. et al. Roquin-2 shares functions with its paralog Roquin-1 in the repression of mRNAs controlling T follicular helper cells and systemic inflammation. Immunity 38, 669–680 (2013).

    CAS  PubMed  Google Scholar 

  46. Minagawa, K. et al. Posttranscriptional modulation of cytokine production in T cells for the regulation of excessive inflammation by TFL. J. Immunol. 192, 1512–1524 (2014).

    CAS  PubMed  Google Scholar 

  47. Hodson, D.J. et al. Deletion of the RNA-binding proteins ZFP36L1 and ZFP36L2 leads to perturbed thymic development and T lymphoblastic leukemia. Nat. Immunol. 11, 717–724 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  48. Kedde, M. & Agami, R. Interplay between microRNAs and RNA-binding proteins determines developmental processes. Cell Cycle 7, 899–903 (2008).

    CAS  PubMed  Google Scholar 

  49. Meisner, N.C. et al. mRNA openers and closers: modulating AU-rich element-controlled mRNA stability by a molecular switch in mRNA secondary structure. ChemBioChem 5, 1432–1447 (2004).

    CAS  PubMed  Google Scholar 

  50. Ray, P.S. et al. A stress-responsive RNA switch regulates VEGFA expression. Nature 457, 915–919 (2009).

    CAS  PubMed  Google Scholar 

  51. Chang, C.H. et al. Posttranscriptional control of T cell effector function by aerobic glycolysis. Cell 153, 1239–1251 (2013).This study establishes links between metabolism and post-transcriptional regulation that direct effector T cell function.

    CAS  PubMed  PubMed Central  Google Scholar 

  52. Venigalla, R.K. & Turner, M. RNA-binding proteins as a point of convergence of the PI3K and p38 MAPK pathways. Front. Immunol. 3, 398 (2012).

    PubMed  PubMed Central  Google Scholar 

  53. Mori, M. et al. Hippo signaling regulates microprocessor and links cell-density-dependent miRNA biogenesis to cancer. Cell 156, 893–906 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  54. Trabucchi, M. et al. The RNA-binding protein KSRP promotes the biogenesis of a subset of microRNAs. Nature 459, 1010–1014 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  55. Bronevetsky, Y. et al. T cell activation induces proteasomal degradation of Argonaute and rapid remodeling of the microRNA repertoire. J. Exp. Med. 210, 417–432 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  56. Uehata, T. et al. Malt1-induced cleavage of regnase-1 in CD4+ helper T cells regulates immune activation. Cell 153, 1036–1049 (2013).

    CAS  PubMed  Google Scholar 

  57. Iwasaki, H. et al. The IκB kinase complex regulates the stability of cytokine-encoding mRNA induced by TLR-IL-1R by controlling degradation of regnase-1. Nat. Immunol. 12, 1167–1175 (2011).

    CAS  PubMed  Google Scholar 

  58. Cano, F., Miranda-Saavedra, D. & Lehner, P.J. RNA-binding E3 ubiquitin ligases: novel players in nucleic acid regulation. Biochem. Soc. Trans. 38, 1621–1626 (2010).

    CAS  PubMed  Google Scholar 

  59. Cano, F. et al. The RNA-binding E3 ubiquitin ligase MEX-3C links ubiquitination with MHC-I mRNA degradation. EMBO J. 31, 3596–3606 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  60. Maruyama, T. et al. Roquin-2 promotes ubiquitin-mediated degradation of ASK1 to regulate stress responses. Sci. Signal. 7, ra8 (2014).

    PubMed  Google Scholar 

  61. Leung, A.K. et al. Poly(ADP-ribose) regulates stress responses and microRNA activity in the cytoplasm. Mol. Cell 42, 489–499 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  62. Shen, Z.J., Esnault, S. & Malter, J.S. The peptidyl-prolyl isomerase Pin1 regulates the stability of granulocyte-macrophage colony-stimulating factor mRNA in activated eosinophils. Nat. Immunol. 6, 1280–1287 (2005).

    CAS  PubMed  Google Scholar 

  63. Sumazin, P. et al. An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma. Cell 147, 370–381 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  64. Keene, J.D. RNA regulons: coordination of post-transcriptional events. Nat. Rev. Genet. 8, 533–543 (2007).

    CAS  PubMed  Google Scholar 

  65. Masuda, K. et al. Arid5a controls IL-6 mRNA stability, which contributes to elevation of IL-6 level in vivo. Proc. Natl. Acad. Sci. USA 110, 9409–9414 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  66. Ho, J.J. & Marsden, P.A. Competition and collaboration between RNA-binding proteins and microRNAs. Wiley Interdiscip. Rev. RNA 5, 69–86 (2014).

    CAS  PubMed  Google Scholar 

  67. Brooks, S.A. & Blackshear, P.J. Tristetraprolin (TTP): interactions with mRNA and proteins, and current thoughts on mechanisms of action. Biochim. Biophys. Acta 1829, 666–679 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  68. Dai, W., Zhang, G. & Makeyev, E.V. RNA-binding protein HuR autoregulates its expression by promoting alternative polyadenylation site usage. Nucleic Acids Res. 40, 787–800 (2012).

    CAS  PubMed  Google Scholar 

  69. Dassi, E. et al. Hyperconserved elements in vertebrate mRNA 3′-UTRs reveal a translational network of RNA-binding proteins controlled by HuR. Nucleic Acids Res. 41, 3201–3216 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  70. Eiring, A.M. et al. miR-328 functions as an RNA decoy to modulate hnRNP E2 regulation of mRNA translation in leukemic blasts. Cell 140, 652–665 (2010).Here a miRNA is found to act by a new mechanism; it functions as a decoy that blocks the interaction of an RBP with target transcripts.

    CAS  PubMed  PubMed Central  Google Scholar 

  71. Clark, M.B. et al. Genome-wide analysis of long noncoding RNA stability. Genome Res. 22, 885–898 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  72. Niazi, F. & Valadkhan, S. Computational analysis of functional long noncoding RNAs reveals lack of peptide-coding capacity and parallels with 3′ UTRs. RNA 18, 825–843 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  73. Hansen, T.B. et al. Natural RNA circles function as efficient microRNA sponges. Nature 495, 384–388 (2013).

    CAS  PubMed  Google Scholar 

  74. Memczak, S. et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 495, 333–338 (2013).

    CAS  PubMed  Google Scholar 

  75. Tay, Y., Rinn, J. & Pandolfi, P.P. The multilayered complexity of ceRNA crosstalk and competition. Nature 505, 344–352 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  76. Kretz, M. et al. Control of somatic tissue differentiation by the long noncoding RNA TINCR. Nature 493, 231–235 (2012).

    PubMed  PubMed Central  Google Scholar 

  77. Yoon, J.H. et al. LincRNA-p21 suppresses target mRNA translation. Mol. Cell 47, 648–655 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  78. Makeyev, E.V., Zhang, J., Carrasco, M.A. & Maniatis, T. The microRNA miR-124 promotes neuronal differentiation by triggering brain-specific alternative pre-mRNA splicing. Mol. Cell 27, 435–448 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  79. Yuan, J., Nguyen, C.K., Liu, X., Kanellopoulou, C. & Muljo, S.A. Lin28b reprograms adult bone marrow hematopoietic progenitors to mediate fetal-like lymphopoiesis. Science 335, 1195–1200 (2012).This article shows the ability of an RBP to reprogram hematopoietic cells, demonstrating the fundamental power of this layer of control.

    CAS  PubMed  PubMed Central  Google Scholar 

  80. Rounbehler, R.J. et al. Tristetraprolin impairs Myc-induced lymphoma and abolishes the malignant state. Cell 150, 563–574 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  81. Heissmeyer, V. & Vogel, K.U. Molecular control of TFH-cell differentiation by Roquin family proteins. Immunol. Rev. 253, 273–289 (2013).

    PubMed  Google Scholar 

  82. Akira, S. Regnase-1, a ribonuclease involved in the regulation of immune responses. Cold Spring Harb. Symp. Quant. Biol. 10.1101/sqb.2013.78.019877 (25 October 2013).

  83. Yiakouvaki, A. et al. Myeloid cell expression of the RNA-binding protein HuR protects mice from pathologic inflammation and colorectal carcinogenesis. J. Clin. Invest. 122, 48–61 (2012).

    CAS  PubMed  Google Scholar 

  84. Simarro, M. et al. The translational repressor T-cell intracellular antigen-1 (TIA-1) is a key modulator of Th2 and Th17 responses driving pulmonary inflammation induced by exposure to house dust mite. Immunol. Lett. 146, 8–14 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  85. Baumjohann, D. & Ansel, K.M. MicroRNA-mediated regulation of T helper cell differentiation and plasticity. Nat. Rev. Immunol. 13, 666–678 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  86. Li, Q.J. et al. miR-181a is an intrinsic modulator of T cell sensitivity and selection. Cell 129, 147–161 (2007).

    CAS  PubMed  Google Scholar 

  87. Ebert, P.J., Jiang, S., Xie, J., Li, Q.J. & Davis, M.M. An endogenous positively selecting peptide enhances mature T cell responses and becomes an autoantigen in the absence of microRNA miR-181a. Nat. Immunol. 10, 1162–1169 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  88. Baumjohann, D. et al. The microRNA cluster miR-17 approximately 92 promotes TFH cell differentiation and represses subset-inappropriate gene expression. Nat. Immunol. 14, 840–848 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  89. Kang, S.G. et al. MicroRNAs of the miR-17 approximately 92 family are critical regulators of TFH differentiation. Nat. Immunol. 14, 849–857 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  90. Jin, H.Y. et al. MicroRNA-1792 plays a causative role in lymphomagenesis by coordinating multiple oncogenic pathways. EMBO J. 32, 2377–2391 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  91. Gracias, D.T. et al. The microRNA miR-155 controls CD8+ T cell responses by regulating interferon signaling. Nat. Immunol. 14, 593–602 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  92. Willingham, A.T. et al. A strategy for probing the function of noncoding RNAs finds a repressor of NFAT. Science 309, 1570–1573 (2005).Refs. 92 and 93 highlight a structural role for noncoding RNA in signal-transduction complexes. It will be interesting to see whether further examples are found.

    CAS  PubMed  Google Scholar 

  93. Sharma, S. et al. Dephosphorylation of the nuclear factor of activated T cells (NFAT) transcription factor is regulated by an RNA-protein scaffold complex. Proc. Natl. Acad. Sci. USA 108, 11381–11386 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  94. Madhani, H.D. The frustrated gene: origins of eukaryotic gene expression. Cell 155, 744–749 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  95. Reineke, L.C. & Lloyd, R.E. Diversion of stress granules and P-bodies during viral infection. Virology 436, 255–267 (2013).

    CAS  PubMed  Google Scholar 

  96. Liu, S. et al. MCPIP1 restricts HIV infection and is rapidly degraded in activated CD4+ T cells. Proc. Natl. Acad. Sci. USA 110, 19083–19088 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  97. Lin, R.J. et al. MCPIP1 ribonuclease exhibits broad-spectrum antiviral effects through viral RNA binding and degradation. Nucleic Acids Res. 41, 3314–3326 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  98. Gao, G., Guo, X. & Goff, S.P. Inhibition of retroviral RNA production by ZAP, a CCCH-type zinc finger protein. Science 297, 1703–1706 (2002).

    CAS  PubMed  Google Scholar 

  99. Hayakawa, S. et al. ZAPS is a potent stimulator of signaling mediated by the RNA helicase RIG-I during antiviral responses. Nat. Immunol. 12, 37–44 (2011).

    CAS  PubMed  Google Scholar 

  100. Lee, H. et al. Zinc-finger antiviral protein mediates retinoic acid inducible gene I-like receptor-independent antiviral response to murine leukemia virus. Proc. Natl. Acad. Sci. USA 110, 12379–12384 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  101. Li, Y., Lu, J., Han, Y., Fan, X. & Ding, S.W. RNA interference functions as an antiviral immunity mechanism in mammals. Science 342, 231–234 (2013).Refs. 101, 102 and 107 advance the understanding of the limited role of small interfering RNAs in antiviral responses.

    CAS  PubMed  Google Scholar 

  102. Maillard, P.V. et al. Antiviral RNA interference in mammalian cells. Science 342, 235–238 (2013).

    CAS  PubMed  Google Scholar 

  103. Cullen, B.R., Cherry, S. & Tenoever, B.R. Is RNA interference a physiologically relevant innate antiviral immune response in mammals? Cell Host Microbe 14, 374–378 (2013).

    CAS  PubMed  Google Scholar 

  104. Cullen, B.R. MicroRNAs as mediators of viral evasion of the immune system. Nat. Immunol. 14, 205–210 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  105. Trobaugh, D.W. et al. RNA viruses can hijack vertebrate microRNAs to suppress innate immunity. Nature 506, 245–248 (2014).

    CAS  PubMed  Google Scholar 

  106. Jopling, C.L., Yi, M., Lancaster, A.M., Lemon, S.M. & Sarnow, P. Modulation of hepatitis C virus RNA abundance by a liver-specific microRNA. Science 309, 1577–1581 (2005).

    CAS  PubMed  Google Scholar 

  107. Seo, G.J. et al. Reciprocal inhibition between intracellular antiviral signaling and the RNAi machinery in mammalian cells. Cell Host Microbe 14, 435–445 (2013).

    CAS  PubMed  Google Scholar 

  108. Rodríguez Pulido, M., Serrano, P., Saiz, M. & Martinez-Salas, E. Foot-and-mouth disease virus infection induces proteolytic cleavage of PTB, eIF3a,b, and PABP RNA-binding proteins. Virology 364, 466–474 (2007).

    PubMed  Google Scholar 

  109. Moon, S.L. et al. A noncoding RNA produced by arthropod-borne flaviviruses inhibits the cellular exoribonuclease XRN1 and alters host mRNA stability. RNA 18, 2029–2040 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  110. Barnhart, M.D., Moon, S.L., Emch, A.W., Wilusz, C.J. & Wilusz, J. Changes in cellular mRNA stability, splicing, and polyadenylation through HuR protein sequestration by a cytoplasmic RNA virus. Cell Rep. 5, 909–917 (2013).

    CAS  PubMed  Google Scholar 

  111. Lee, N., Pimienta, G. & Steitz, J.A. AUF1/hnRNP D is a novel protein partner of the EBER1 noncoding RNA of Epstein-Barr virus. RNA 18, 2073–2082 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  112. Cazalla, D., Yario, T. & Steitz, J.A. Down-regulation of a host microRNA by a Herpesvirus saimiri noncoding RNA. Science 328, 1563–1566 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  113. Marcinowski, L. et al. Degradation of cellular mir-27 by a novel, highly abundant viral transcript is important for efficient virus replication in vivo. PLoS Pathog. 8, e1002510 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  114. Lee, S. et al. Selective degradation of host microRNAs by an intergenic HCMV noncoding RNA accelerates virus production. Cell Host Microbe 13, 678–690 (2013).This article describes a viral noncoding RNA that is needed to promote the production of virus under lytic conditions and mediates the degradation of a host-cell miRNA.

    CAS  PubMed  Google Scholar 

  115. McFarland, A.P. et al. The favorable IFNL3 genotype escapes mRNA decay mediated by AU-rich elements and hepatitis C virus–induced microRNAs. Nat. Immunol. 15, 72–79 (2014).

    CAS  PubMed  Google Scholar 

  116. LaMonte, G. et al. Translocation of sickle cell erythrocyte microRNAs into Plasmodium falciparum inhibits parasite translation and contributes to malaria resistance. Cell Host Microbe 12, 187–199 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

We thank M. Linterman, P. Katsikis, R. Newman and L. Webb for advice and comments on the manuscript. Supported by the Biotechnology and Biological Sciences Research Council, the Medical Research Council (M.T. and E.V.) and Leukaemia and Lymphoma Research (A.G.).

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Turner, M., Galloway, A. & Vigorito, E. Noncoding RNA and its associated proteins as regulatory elements of the immune system. Nat Immunol 15, 484–491 (2014). https://doi.org/10.1038/ni.2887

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