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Zcchc11-dependent uridylation of microRNA directs cytokine expression

Nature Cell Biology volume 11, pages 1157–1163 (2009)Cite this article

Abstract

Mounting an effective host immune response without incurring inflammatory injury requires the precise regulation of cytokine expression1,2. To achieve this, cytokine mRNAs are post-transcriptionally regulated by diverse RNA-binding proteins and microRNAs (miRNAs) targeting their 3′ untranslated regions (UTRs)3,4. Zcchc11 (zinc-finger, CCHC domain-containing protein 11) contains RNA-interacting motifs5, and has been implicated in signalling pathways involved in cytokine expression6. The nature of the Zcchc11 protein and how it influences cytokine expression are unknown. Here we show that Zcchc11 directs cytokine expression by uridylating cytokine-targeting miRNAs. Zcchc11 is a ribonucleotidyltransferase with a preference for uridine and is essential for maintaining the poly(A) tail length and stability of transcripts for interleukin-6 (IL-6) and other specific cytokines. The miR-26 family of miRNAs targets IL-6, and the addition of terminal uridines to the miR-26 3′ end abrogates IL-6 repression. Whereas 78% of miR-26a sequences in control cells contained 1–3 uridines on their 3′ ends, less than 0.1% did so in Zcchc11-knockdown cells. Thus, Zcchc11 fine tunes IL-6 production by uridylating miR-26a, which we propose is an enzymatic modification of the terminal nucleotide sequence of mature miRNA as a means to regulate gene expression.

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Figure 1: Zcchc11 is a uridyltransferase.
Figure 2: Zcchc11 knockdown alters cytokine mRNA stability and expression.
Figure 3: The miR-26 family regulates IL-6 expression.
Figure 4: Zcchc11-dependent uridylation of miR-26 abrogates silencing of IL-6 mRNA.

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References

  1. Nathan, C. Points of control in inflammation. Nature 420, 846–852 (2002).

    Article  CAS  Google Scholar 

  2. Mizgerd, J. P. Acute lower respiratory tract infection. N. Engl. J. Med. 358, 716–727 (2008).

    Article  CAS  Google Scholar 

  3. Jing, Q. et al. Involvement of microRNA in AU-rich element-mediated mRNA instability. Cell 120, 623–634 (2005).

    Article  CAS  Google Scholar 

  4. Stoecklin, G. & Anderson, P. Posttranscriptional mechanisms regulating the inflammatory response. Adv. Immunol. 89, 1–37 (2006).

    Article  CAS  Google Scholar 

  5. Aravind, L. & Koonin, E. V. DNA polymerase β-like nucleotidyltransferase superfamily: identification of three new families, classification and evolutionary history. Nucleic Acids Res. 27, 1609–1618 (1999).

    Article  CAS  Google Scholar 

  6. Minoda, Y. et al. A novel Zinc finger protein, ZCCHC11, interacts with TIFA and modulates TLR signaling. Biochem. Biophys. Res. Commun. 344, 1023–1030 (2006).

    Article  CAS  Google Scholar 

  7. Marchler-Bauer, A. et al. CDD: a conserved domain database for interactive domain family analysis. Nucleic Acids Res. 35, D237–240 (2007).

    Article  CAS  Google Scholar 

  8. Laity, J. H., Lee, B. M. & Wright, P. E. Zinc finger proteins: new insights into structural and functional diversity. Curr. Opin. Struct. Biol. 11, 39–46 (2001).

    Article  CAS  Google Scholar 

  9. Amarasinghe, G. K. et al. NMR structure of the HIV-1 nucleocapsid protein bound to stem-loop SL2 of the psi-RNA packaging signal. Implications for genome recognition. J. Mol. Biol. 301, 491–511 (2000).

    Article  CAS  Google Scholar 

  10. Wang, L., Eckmann, C. R., Kadyk, L. C., Wickens, M. & Kimble, J. A regulatory cytoplasmic poly(A) polymerase in Caenorhabditis elegans. Nature 419, 312–316 (2002).

    Article  CAS  Google Scholar 

  11. Saitoh, S. et al. Cid13 is a cytoplasmic poly(A) polymerase that regulates ribonucleotide reductase mRNA. Cell 109, 563–573 (2002).

    Article  CAS  Google Scholar 

  12. Read, R. L., Martinho, R. G., Wang, S. W., Carr, A. M. & Norbury, C. J. Cytoplasmic poly(A) polymerases mediate cellular responses to S phase arrest. Proc. Natl Acad. Sci. USA 99, 12079–12084 (2002).

    Article  CAS  Google Scholar 

  13. Martin, G. & Keller, W. Mutational analysis of mammalian poly(A) polymerase identifies a region for primer binding and catalytic domain, homologous to the family X polymerases, and to other nucleotidyltransferases. EMBO J. 15, 2593–2603 (1996).

    Article  CAS  Google Scholar 

  14. Rissland, O. S., Mikulasova, A. & Norbury, C. J. Efficient RNA polyuridylation by noncanonical poly(A) polymerases. Mol Cell Biol 27, 3612–3624 (2007).

    Article  CAS  Google Scholar 

  15. Kwak, J. E. & Wickens, M. A family of poly(U) polymerases. RNA 13, 860–867 (2007).

    Article  CAS  Google Scholar 

  16. Meyer, S., Temme, C. & Wahle, E. Messenger RNA turnover in eukaryotes: pathways and enzymes. Crit. Rev. Biochem. Mol. Biol. 39, 197–216 (2004).

    Article  CAS  Google Scholar 

  17. de Moor, C. H., Meijer, H. & Lissenden, S. Mechanisms of translational control by the 3′ UTR in development and differentiation. Semin. Cell Dev. Biol. 16, 49–58 (2005).

    Article  CAS  Google Scholar 

  18. Salles, F. J., Richards, W. G. & Strickland, S. Assaying the polyadenylation state of mRNAs. Methods 17, 38–45 (1999).

    Article  CAS  Google Scholar 

  19. Wu, L., Fan, J. & Belasco, J. G. MicroRNAs direct rapid deadenylation of mRNA. Proc. Natl Acad. Sci. USA 103, 4034–4039 (2006).

    Article  CAS  Google Scholar 

  20. Behm-Ansmant, I. et al. mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes. Genes Dev. 20, 1885–1898 (2006).

    Article  CAS  Google Scholar 

  21. Seitz, H., Ghildiyal, M. & Zamore, P. D. Argonaute loading improves the 5′ precision of both MicroRNAs and their miRNA strands in flies. Curr. Biol. 18, 147–151 (2008).

    Article  CAS  Google Scholar 

  22. Morin, R. D. et al. Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res. 18, 610–621 (2008).

    Article  CAS  Google Scholar 

  23. Landgraf, P. et al. A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 129, 1401–1414 (2007).

    Article  CAS  Google Scholar 

  24. Katoh, T. et al. Selective stabilization of mammalian microRNAs by 3′ adenylation mediated by the cytoplasmic poly(A) polymerase GLD-2. Genes Dev. 23, 433–438 (2009).

    Article  CAS  Google Scholar 

  25. Friedman, R. C., Farh, K. K., Burge, C. B. & Bartel, D. P. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res. 19, 92–105 (2009).

    Article  CAS  Google Scholar 

  26. Grimson, A. et al. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol. Cell 27, 91–105 (2007).

    Article  CAS  Google Scholar 

  27. Lewis, B. P., Burge, C. B. & Bartel, D. P. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120, 15–20 (2005).

    Article  CAS  Google Scholar 

  28. Nielsen, C. B. et al. Determinants of targeting by endogenous and exogenous microRNAs and siRNAs. RNA 13, 1894–1910 (2007).

    Article  CAS  Google Scholar 

  29. Wu, H. et al. miRNA profiling of naive, effector and memory CD8 T cells. PLoS ONE 2, e1020 (2007).

    Article  Google Scholar 

  30. Hutvagner, G., Simard, M. J., Mello, C. C. & Zamore, P. D. Sequence-specific inhibition of small RNA function. PLoS Biol. 2, E98 (2004).

    Article  Google Scholar 

  31. Meister, G., Landthaler, M., Dorsett, Y. & Tuschl, T. Sequence-specific inhibition of microRNA- and siRNA-induced RNA silencing. RNA 10, 544–550 (2004).

    Article  CAS  Google Scholar 

  32. Hua, Z. et al. MiRNA-directed regulation of VEGF and other angiogenic factors under hypoxia. PLoS ONE 1, e116 (2006).

    Article  Google Scholar 

  33. Heil, F. et al. Species-specific recognition of single-stranded RNA via toll-like receptor 7 and 8. Science 303, 1526–1529 (2004).

    Article  CAS  Google Scholar 

  34. Ruby, J. G. et al. Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell 127, 1193–1207 (2006).

    Article  CAS  Google Scholar 

  35. Ruby, J. G., Jan, C. H. & Bartel, D. P. Intronic microRNA precursors that bypass Drosha processing. Nature 448, 83–86 (2007).

    Article  CAS  Google Scholar 

  36. Neilson, J. R., Zheng, G. X., Burge, C. B. & Sharp, P. A. Dynamic regulation of miRNA expression in ordered stages of cellular development. Genes Dev. 21, 578–589 (2007).

    Article  CAS  Google Scholar 

  37. Shen, B. & Goodman, H. M. Uridine addition after microRNA-directed cleavage. Science 306, 997 (2004).

    Article  CAS  Google Scholar 

  38. Cheng, A. M., Byrom, M. W., Shelton, J. & Ford, L. P. Antisense inhibition of human miRNAs and indications for an involvement of miRNA in cell growth and apoptosis. Nucleic Acids Res. 33, 1290–1297 (2005).

    Article  CAS  Google Scholar 

  39. Lykke-Andersen, J. Identification of a human decapping complex associated with hUpf proteins in nonsense-mediated decay. Mol. Cell Biol. 22, 8114–8121 (2002).

    Article  CAS  Google Scholar 

  40. Schmittgen, T. D. et al. Quantitative reverse transcription-polymerase chain reaction to study mRNA decay: comparison of endpoint and real-time methods. Anal. Biochem. 285, 194–204 (2000).

    Article  CAS  Google Scholar 

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Acknowledgements

We thank P. Sharp for access to the Koch Institute bioinformatics core and C. Whittaker, R. Cook and A. Leshinsky for outstanding Illumina sequence collection and processing. Illumina analysis pipeline was supported by a National Cancer Institute PO1 grant (CA42063) to P.A.S. We thank K. Doud for technical assistance and I. Kramnik for help with the Luminex bead array. M.R.J. was supported by an American Physiological Society Fellowship in Physiological Genomics and a Parker B. Francis fellowship. L.J.Q. was supported by an American Lung Association Senior Research Training Fellowship and an NIH grant (K99 HL092956). J.R.N. was supported by an NIH grant (K99 CA131474). Studies were supported by NIH grants (R01 HL068153, R01 HL079392 and P01 ES00002).

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  1. Dieter A. Wolf

    Present address: Current address: Signal Transduction Program, Burnham Institute for Medical Research, La Jolla, CA 92037, USA.,

Authors and Affiliations

  1. The Pulmonary Center, Boston University School of Medicine, Boston, 102118, MA, USA

    Matthew R. Jones, Lee J. Quinton, Matthew T. Blahna & Joseph P. Mizgerd

  2. Molecular and Integrative Physiological Sciences, Boston, 02115, MA, USA

    Matthew R. Jones, Lee J. Quinton, Matthew T. Blahna & Joseph P. Mizgerd

  3. Department of Genetics and Complex Diseases and NIEHS Center Proteomics Facility, Harvard School of Public Health, Boston, 02115, MA, USA

    Suneng Fu, Alexander R. Ivanov & Dieter A. Wolf

  4. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, 02139, MA, USA

    Joel R. Neilson

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Contributions

M.R.J. conceived this line of investigation and designed, performed and analysed most of the experiments. L.I.Q. and M.T.B. designed, performed and analysed some experiments and assisted with others. J.R.N. directed the deep sequencing study and helped interpret results. S.F. contributed to recombinant protein generation and functional assessment. A.R.I. performed proteomic experiments, identifying Zcchc11 in infected lungs. D.A.W. directed proteomic experiments and contributed to study design and interpretation. J.P.M. designed, analysed and directed the studies and guided the research programme. The manuscript was written by M.R.J., L.I.Q., M.T.B and J.P.M.

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Correspondence to Joseph P. Mizgerd.

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The authors declare no competing financial interests.

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Jones, M., Quinton, L., Blahna, M. et al. Zcchc11-dependent uridylation of microRNA directs cytokine expression. Nat Cell Biol 11, 1157–1163 (2009). https://doi.org/10.1038/ncb1931

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