Article | Published:

Ribosomal frameshifting in the CCR5 mRNA is regulated by miRNAs and the NMD pathway

Nature volume 512, pages 265269 (21 August 2014) | Download Citation

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Abstract

Programmed −1 ribosomal frameshift (−1 PRF) signals redirect translating ribosomes to slip back one base on messenger RNAs. Although well characterized in viruses, how these elements may regulate cellular gene expression is not understood. Here we describe a −1 PRF signal in the human mRNA encoding CCR5, the HIV-1 co-receptor. CCR5 mRNA-mediated −1 PRF is directed by an mRNA pseudoknot, and is stimulated by at least two microRNAs. Mapping the mRNA–miRNA interaction suggests that formation of a triplex RNA structure stimulates −1 PRF. A −1 PRF event on the CCR5 mRNA directs translating ribosomes to a premature termination codon, destabilizing it through the nonsense-mediated mRNA decay pathway. At least one additional mRNA decay pathway is also involved. Functional −1 PRF signals that seem to be regulated by miRNAs are also demonstrated in mRNAs encoding six other cytokine receptors, suggesting a novel mode through which immune responses may be fine-tuned in mammalian cells.

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Acknowledgements

This work was supported by grants to J.D.D. from the National Institutes of Health (5 R01GM058859, R21GM068123) and from the National Science Foundation (MCB-0084559). A.T.B. was supported by NIH/NIAID T32 AI051967, and a University of Maryland College of CMNS Hockmeyer Fellowship. S.O.S. was supported by NIH/NIGMS T32GM080201. This publication has also been funded in part with federal funds from the Frederick National Laboratory for Cancer Research, NIH, under Contract HHSN261200800001E to W.K.K. This research was supported in part by the Intramural Research Program of the National Institutes of Health, Center for Cancer Research to B.A.S. The content of this publication does not necessarily reflect the views or policies of the DHHS, nor does mention of trade names, commercial products, or organizations imply endorsement by the US Government.

Author information

Author notes

    • Ashton Trey Belew
    •  & Arturas Meskauskas

    These authors contributed equally to this work.

    • Sergey O. Sulima

    Present address: VIB Center for the Biology of Disease, KU Leuven, Campus Gasthuisberg, Herestraat 49, bus 602, 3000 Leuven, Belgium.

Affiliations

  1. Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, USA

    • Ashton Trey Belew
    • , Arturas Meskauskas
    • , Sharmishtha Musalgaonkar
    • , Vivek M. Advani
    • , Sergey O. Sulima
    •  & Jonathan D. Dinman
  2. Department of Biotechnology and Microbiology, Vilnius University, Vilnius, LT 03101, Lithuania

    • Arturas Meskauskas
  3. Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA

    • Wojciech K. Kasprzak
  4. Basic Research Laboratory, National Cancer Institute, Frederick, Maryland 21702, USA

    • Bruce A. Shapiro

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Contributions

A.T.B. designed and performed experiments (Figs 1a, 3a, b, 4b, c, 5a, b, e and Extended Data Figs 1a, 2b, 4b, c, 5b–d and 6), analysed data, and helped in editing the manuscript. A.M. designed and performed experiments and analysed data (Fig. 4a, d and Extended Data Figs 2c, d, 3b,c, 5 and 6). S.M. made constructs and performed the experiment shown in Fig. 1b, and helped with experiments. V.M.A. designed, performed and analysed the data collected in the experiments shown in Figs 3c, 5c, d, and assisted with data shown in Figs 3b, 5a, b, and Extended Data Fig. 5d. S.O.S. assisted with sample preparation and data collection. W.K.K. and B.A.S. performed all of the molecular dynamics simulations and molecular modelling. J.D.D. conceived and directed the project, designed experiments and wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Jonathan D. Dinman.

The sequences determined in this work are deposited in the NCBI Nucleotide database; a list is available as Supplementary Information.

Extended data

Supplementary information

CSV files

  1. 1.

    Supplementary Data

    This file contains the sequences determined in this work. They are also deposited in the NCBI Nucleotide database.

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DOI

https://doi.org/10.1038/nature13429

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