Abstract

Dynamic post-transcriptional control of RNA expression by RNA-binding proteins (RBPs) is critical during immune response. ZFP36 RBPs are prominent inflammatory regulators linked to autoimmunity and cancer, but functions in adaptive immunity are less clear. We used HITS-CLIP to define ZFP36 targets in mouse T cells, revealing unanticipated actions in regulating T cell activation, proliferation, and effector functions. Transcriptome and ribosome profiling showed that ZFP36 represses mRNA target abundance and translation, notably through novel AU-rich sites in coding sequence. Functional studies revealed that ZFP36 regulates early T cell activation kinetics cell autonomously, by attenuating activation marker expression, limiting T cell expansion, and promoting apoptosis. Strikingly, loss of ZFP36 in vivo accelerated T cell responses to acute viral infection and enhanced anti-viral immunity. These findings uncover a critical role for ZFP36 RBPs in restraining T cell expansion and effector functions, and suggest ZFP36 inhibition as a strategy to enhance immune-based therapies.

Data availability

Sequencing data are in GEO under the accession code GSE96076

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Michael J Moore

    Laboratory of Molecular Neuro-Onology, The Rockefeller University, New York, United States
    Competing interests
    Michael J Moore, currently affiliated with Regeneron Phrmaceuticals. The author has no other financial competing interests to declare.
  2. Nathalie E Blachere

    Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, United States
    Competing interests
    No competing interests declared.
  3. John J Fak

    Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, United States
    Competing interests
    No competing interests declared.
  4. Christopher Y Park

    Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, United States
    Competing interests
    No competing interests declared.
  5. Kirsty Sawicka

    Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, United States
    Competing interests
    No competing interests declared.
  6. Salina Parveen

    Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, United States
    Competing interests
    No competing interests declared.
  7. Ilana Zucker-Scharff

    Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, United States
    Competing interests
    No competing interests declared.
  8. Bruno Moltedo

    The Immunology Program, Memorial Sloan Kettering Cancer Center, New York, United States
    Competing interests
    No competing interests declared.
  9. Alexander Y Rudensky

    The Immunology Program, Memorial Sloan Kettering Cancer Center, New York, United States
    Competing interests
    No competing interests declared.
  10. Robert B Darnell

    Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, United States
    For correspondence
    darnelr@rockefeller.edu
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5134-8088

Funding

National Institutes of Health

  • Robert B Darnell

Starr Foundation

  • Robert B Darnell

Jane Coffin Childs Memorial Fund for Medical Research

  • Michael J Moore

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Animal experimentation: All mouse strains were maintained at the University of California, San Francisco (UCSF) specific pathogen-free animal facility under protocol number AN110094. All animal protocols were approved by and in accordance with the guidelines established by the Institutional Animal Care and Use Committee and Laboratory Animal Resource Center

Copyright

© 2018, Moore et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 8,568
    views
  • 988
    downloads
  • 110
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Michael J Moore
  2. Nathalie E Blachere
  3. John J Fak
  4. Christopher Y Park
  5. Kirsty Sawicka
  6. Salina Parveen
  7. Ilana Zucker-Scharff
  8. Bruno Moltedo
  9. Alexander Y Rudensky
  10. Robert B Darnell
(2018)
ZFP36 RNA-binding proteins restrain T-cell activation and anti-viral immunity
eLife 7:e33057.
https://doi.org/10.7554/eLife.33057

Share this article

https://doi.org/10.7554/eLife.33057

Further reading

    1. Chromosomes and Gene Expression
    Carmina Lichauco, Eric J Foss ... Antonio Bedalov
    Research Article

    The association between late replication timing and low transcription rates in eukaryotic heterochromatin is well known, yet the specific mechanisms underlying this link remain uncertain. In Saccharomyces cerevisiae, the histone deacetylase Sir2 is required for both transcriptional silencing and late replication at the repetitive ribosomal DNA (rDNA) arrays. We have previously reported that in the absence of SIR2, a de-repressed RNA PolII repositions MCM replicative helicases from their loading site at the ribosomal origin, where they abut well-positioned, high-occupancy nucleosomes, to an adjacent region with lower nucleosome occupancy. By developing a method that can distinguish activation of closely spaced MCM complexes, here we show that the displaced MCMs at rDNA origins have increased firing propensity compared to the nondisplaced MCMs. Furthermore, we found that both activation of the repositioned MCMs and low occupancy of the adjacent nucleosomes critically depend on the chromatin remodeling activity of FUN30. Our study elucidates the mechanism by which Sir2 delays replication timing, and it demonstrates, for the first time, that activation of a specific replication origin in vivo relies on the nucleosome context shaped by a single chromatin remodeler.

    1. Chromosomes and Gene Expression
    2. Structural Biology and Molecular Biophysics
    Liza Dahal, Thomas GW Graham ... Xavier Darzacq
    Research Article

    Type II nuclear receptors (T2NRs) require heterodimerization with a common partner, the retinoid X receptor (RXR), to bind cognate DNA recognition sites in chromatin. Based on previous biochemical and overexpression studies, binding of T2NRs to chromatin is proposed to be regulated by competition for a limiting pool of the core RXR subunit. However, this mechanism has not yet been tested for endogenous proteins in live cells. Using single-molecule tracking (SMT) and proximity-assisted photoactivation (PAPA), we monitored interactions between endogenously tagged RXR and retinoic acid receptor (RAR) in live cells. Unexpectedly, we find that higher expression of RAR, but not RXR, increases heterodimerization and chromatin binding in U2OS cells. This surprising finding indicates the limiting factor is not RXR but likely its cadre of obligate dimer binding partners. SMT and PAPA thus provide a direct way to probe which components are functionally limiting within a complex TF interaction network providing new insights into mechanisms of gene regulation in vivo with implications for drug development targeting nuclear receptors.