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Zcchc11-dependent uridylation of microRNA directs cytokine expression

Nature Cell Biology volume 11, pages 11571163 (2009) | Download Citation

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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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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).

Author information

Author notes

    • Dieter A. Wolf

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

Affiliations

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

    • Matthew R. Jones
    • , Lee J. Quinton
    • , Matthew T. Blahna
    •  & Joseph P. Mizgerd
  2. Molecular and Integrative Physiological Sciences, Boston, MA 02115, 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, MA 02115, USA.

    • Suneng Fu
    • , Alexander R. Ivanov
    •  & Dieter A. Wolf
  4. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, 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.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Joseph P. Mizgerd.

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DOI

https://doi.org/10.1038/ncb1931

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