Aire-dependent genes undergo Clp1-mediated 3'UTR shortening associated with higher transcript stability in the thymus

  1. Clotilde Guyon
  2. Nada Jmari
  3. Francine Padonou
  4. Yen-Chin Li
  5. Olga Ucar
  6. Noriyuki Fujikado
  7. Fanny Coulpier
  8. Christophe Blanchet
  9. David E Root
  10. Matthieu Giraud  Is a corresponding author
  1. Institut Cochin, INSERM U1016, France
  2. Université de Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, France
  3. German Cancer Research Center, Germany
  4. Harvard Medical School, United States
  5. Institut de Biologie de l'Ecole Normale Supérieure, France
  6. Institut Français de Bioinformatique, CNRS UMS 3601, France
  7. Broad Institute of Harvard and MIT, United States

Abstract

The ability of the immune system to avoid autoimmune disease relies on tolerization of thymocytes to self-antigens whose expression and presentation by thymic medullary epithelial cells (mTECs) is controlled predominantly by Aire at the transcriptional level and possibly regulated at other unrecognized levels. Aire-sensitive gene expression is influenced by several molecular factors, some of which belong to the 3'end processing complex, suggesting they might impact transcript stability and levels through an effect on 3'UTR shortening. We discovered that Aire-sensitive genes display a pronounced preference for short-3'UTR transcript isoforms in mTECs, a feature preceding Aire's expression and correlated with the preferential selection of proximal polyA sites by the 3'end processing complex. Through an RNAi screen and generation of a lentigenic mouse, we found that one factor, Clp1, promotes 3'UTR shortening associated with higher transcript stability and expression of Aire-sensitive genes, revealing a post-transcriptional level of control of Aire-activated expression in mTECs.

Data availability

All RNAseq and microarray data are deposited in the NCBI Gene Expression Omnibus database (GEO).

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

Article and author information

Author details

  1. Clotilde Guyon

    Immunology, Institut Cochin, INSERM U1016, Paris, France
    Competing interests
    The authors declare that no competing interests exist.
  2. Nada Jmari

    Immunology, Institut Cochin, INSERM U1016, Paris, France
    Competing interests
    The authors declare that no competing interests exist.
  3. Francine Padonou

    Université de Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France
    Competing interests
    The authors declare that no competing interests exist.
  4. Yen-Chin Li

    Immunology, Institut Cochin, INSERM U1016, Paris, France
    Competing interests
    The authors declare that no competing interests exist.
  5. Olga Ucar

    Developmental Immunology, German Cancer Research Center, Heidelberg, Germany
    Competing interests
    The authors declare that no competing interests exist.
  6. Noriyuki Fujikado

    Department of Microbiology and Immunobiology, Harvard Medical School, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Fanny Coulpier

    Genomic platform, Institut de Biologie de l'Ecole Normale Supérieure, Paris, France
    Competing interests
    The authors declare that no competing interests exist.
  8. Christophe Blanchet

    IFB-Core, Institut Français de Bioinformatique, CNRS UMS 3601, Evry, France
    Competing interests
    The authors declare that no competing interests exist.
  9. David E Root

    Broad Institute of Harvard and MIT, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  10. Matthieu Giraud

    Université de Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France
    For correspondence
    matthieu.giraud@inserm.fr
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1208-9677

Funding

Agence Nationale de la Recherche (Research grant,2011-CHEX-001-R12004KK)

  • Matthieu Giraud

European Commission (Career Integration Grant,CIG PCIG9-GA-2011-294212)

  • Matthieu Giraud

Agence Nationale de la Recherche (Investissements d'Avenir,ANR-10-INBS-09)

  • Fanny Coulpier

Agence Nationale de la Recherche (Investissements d'Avenir,ANR-11-INBS-0013)

  • Christophe Blanchet

Fondation pour la Recherche Médicale (Graduate Student Fellowship,FDT20150532551)

  • Clotilde Guyon

Fondation pour la Recherche Médicale (Bioinformatics engineer grant)

  • Yen-Chin Li

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

Ethics

Animal experimentation: Mice were housed, bred and manipulated in specific-pathogen-free conditions at Cochin Institute according to the guidelines of the French Veterinary Department and under procedures approved by the Paris-Descartes Ethical Committee for Animal Experimentation (decision CEEA34.MG.021.11 or APAFIS #3683 No 2015062411489297 for lentigenic mouse generation)

Copyright

© 2020, Guyon 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

  • 1,256
    views
  • 165
    downloads
  • 14
    citations

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

Download links

Share this article

https://doi.org/10.7554/eLife.52985

Further reading

    1. Genetics and Genomics
    Yi Li, Long Gong ... Shangbang Gao
    Research Article

    Resistance to anthelmintics, particularly the macrocyclic lactone ivermectin (IVM), presents a substantial global challenge for parasite control. We found that the functional loss of an evolutionarily conserved E3 ubiquitin ligase, UBR-1, leads to IVM resistance in Caenorhabditis elegans. Multiple IVM-inhibiting activities, including viability, body size, pharyngeal pumping, and locomotion, were significantly ameliorated in various ubr-1 mutants. Interestingly, exogenous application of glutamate induces IVM resistance in wild-type animals. The sensitivity of all IVM-affected phenotypes of ubr-1 is restored by eliminating proteins associated with glutamate metabolism or signaling: GOT-1, a transaminase that converts aspartate to glutamate, and EAT-4, a vesicular glutamate transporter. We demonstrated that IVM-targeted GluCls (glutamate-gated chloride channels) are downregulated and that the IVM-mediated inhibition of serotonin-activated pharynx Ca2+ activity is diminished in ubr-1. Additionally, enhancing glutamate uptake in ubr-1 mutants through ceftriaxone completely restored their IVM sensitivity. Therefore, UBR-1 deficiency-mediated aberrant glutamate signaling leads to ivermectin resistance in C. elegans.

    1. Genetics and Genomics
    Minsoo Noh, Xiangguo Che ... Sihoon Lee
    Research Article

    Osteoporosis, characterized by reduced bone density and strength, increases fracture risk, pain, and limits mobility. Established therapies of parathyroid hormone (PTH) analogs effectively promote bone formation and reduce fractures in severe osteoporosis, but their use is limited by potential adverse effects. In the pursuit of safer osteoporosis treatments, we investigated R25CPTH, a PTH variant wherein the native arginine at position 25 is substituted by cysteine. These studies were prompted by our finding of high bone mineral density in a hypoparathyroidism patient with the R25C homozygous mutation, and we explored its effects on PTH type-1 receptor (PTH1R) signaling in cells and bone metabolism in mice. Our findings indicate that R25CPTH(1–84) forms dimers both intracellularly and extracellularly, and the synthetic dimeric peptide, R25CPTH(1–34), exhibits altered activity in PTH1R-mediated cyclic AMP (cAMP) response. Upon a single injection in mice, dimeric R25CPTH(1–34) induced acute calcemic and phosphaturic responses comparable to PTH(1–34). Furthermore, repeated daily injections increased calvarial bone thickness in intact mice and improved trabecular and cortical bone parameters in ovariectomized (OVX) mice, akin to PTH(1–34). The overall results reveal a capacity of a dimeric PTH peptide ligand to activate the PTH1R in vitro and in vivo as PTH, suggesting a potential path of therapeutic PTH analog development.