Aire-dependent genes undergo Clp1-mediated 3'UTR shortening associated with higher transcript stability in the thymus
- Institut Cochin, INSERM U1016, France
- Centre de Recherche en Transplantation et Immunologie, INSERM U1064, France
- German Cancer Research Center, Germany
- Harvard Medical School, United States
- Institut de Biologie de l'Ecole Normale Supérieure, France
- Institut Français de Bioinformatique, CNRS UMS 3601, France
- 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).
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WT and Aire-KO mouse MEChi RNAseq profilingNCBI Gene Expression Omnibus, GSE140683.
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RNAseq profiling of Aire and Ctr-transfected HEK293 cellsNCBI Gene Expression Omnibus, GSE140738.
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Stability of Aire-upregulated and Aire-neutral transcripts in medullary thymic epithelial cellsNCBI Gene Expression Omnibus, GSE140815.
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Clp1 knockdown lentigenic mouse generationNCBI Gene Expression Omnibus, GSE140878.
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RNAseq profiling of Ctr and CLP1 knockdown HEK293 cellsNCBI Gene Expression Omnibus, GSE140993.
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RNAseq profiling of Ctr and CLP1 knockdown HEK293 cellsNCBI Gene Expression Omnibus, GSE141118.
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PAR-CLIP CstF-64NCBI Gene Expression Omnibus, GSM917676.
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Aire-KO MEChi RNAseq profilingNCBI Gene Expression Omnibus, GSE87133.
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Sirt1 is essential for Aire-mediated induction of central immunological toleranceNCBI Gene Expression Omnibus, GSE68190.
Article and author information
Author details
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.
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Aire-dependent genes undergo Clp1-mediated 3'UTR shortening associated with higher transcript stability in the thymus
eLife 9:e52985.
https://doi.org/10.7554/eLife.52985
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