Aire-dependent genes undergo Clp1-mediated 3'UTR shortening associated with higher transcript stability in the thymus
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).
-
WT and Aire-KO mouse MEChi RNAseq profilingNCBI Gene Expression Omnibus, GSE140683.
-
RNAseq profiling of Aire and Ctr-transfected HEK293 cellsNCBI Gene Expression Omnibus, GSE140738.
-
Stability of Aire-upregulated and Aire-neutral transcripts in medullary thymic epithelial cellsNCBI Gene Expression Omnibus, GSE140815.
-
Clp1 knockdown lentigenic mouse generationNCBI Gene Expression Omnibus, GSE140878.
-
RNAseq profiling of Ctr and CLP1 knockdown HEK293 cellsNCBI Gene Expression Omnibus, GSE140993.
-
RNAseq profiling of Ctr and CLP1 knockdown HEK293 cellsNCBI Gene Expression Omnibus, GSE141118.
-
PAR-CLIP CstF-64NCBI Gene Expression Omnibus, GSM917676.
-
Aire-KO MEChi RNAseq profilingNCBI Gene Expression Omnibus, GSE87133.
-
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.
Reviewing Editor
- Clare Blackburn, MRC Centre for Regenerative Medicine, University of Edinburgh, United Kingdom
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)
Version history
- Received: October 23, 2019
- Accepted: April 24, 2020
- Accepted Manuscript published: April 27, 2020 (version 1)
- Accepted Manuscript updated: April 29, 2020 (version 2)
- Version of Record published: May 7, 2020 (version 3)
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
-
- 1,201
- views
-
- 158
- downloads
-
- 13
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
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)
Further reading
-
- Computational and Systems Biology
- Genetics and Genomics
Runs-of-homozygosity (ROH) segments, contiguous homozygous regions in a genome were traditionally linked to families and inbred populations. However, a growing literature suggests that ROHs are ubiquitous in outbred populations. Still, most existing genetic studies of ROH in populations are limited to aggregated ROH content across the genome, which does not offer the resolution for mapping causal loci. This limitation is mainly due to a lack of methods for the efficient identification of shared ROH diplotypes. Here, we present a new method, ROH-DICE (runs-of-homozygous diplotype cluster enumerator), to find large ROH diplotype clusters, sufficiently long ROHs shared by a sufficient number of individuals, in large cohorts. ROH-DICE identified over 1 million ROH diplotypes that span over 100 single nucleotide polymorphisms (SNPs) and are shared by more than 100 UK Biobank participants. Moreover, we found significant associations of clustered ROH diplotypes across the genome with various self-reported diseases, with the strongest associations found between the extended human leukocyte antigen (HLA) region and autoimmune disorders. We found an association between a diplotype covering the homeostatic iron regulator (HFE) gene and hemochromatosis, even though the well-known causal SNP was not directly genotyped or imputed. Using a genome-wide scan, we identified a putative association between carriers of an ROH diplotype in chromosome 4 and an increase in mortality among COVID-19 patients (p-value = 1.82 × 10−11). In summary, our ROH-DICE method, by calling out large ROH diplotypes in a large outbred population, enables further population genetics into the demographic history of large populations. More importantly, our method enables a new genome-wide mapping approach for finding disease-causing loci with multi-marker recessive effects at a population scale.
-
- Chromosomes and Gene Expression
- Genetics and Genomics
Members of the diverse heterochromatin protein 1 (HP1) family play crucial roles in heterochromatin formation and maintenance. Despite the similar affinities of their chromodomains for di- and tri-methylated histone H3 lysine 9 (H3K9me2/3), different HP1 proteins exhibit distinct chromatin-binding patterns, likely due to interactions with various specificity factors. Previously, we showed that the chromatin-binding pattern of the HP1 protein Rhino, a crucial factor of the Drosophila PIWI-interacting RNA (piRNA) pathway, is largely defined by a DNA sequence-specific C2H2 zinc finger protein named Kipferl (Baumgartner et al., 2022). Here, we elucidate the molecular basis of the interaction between Rhino and its guidance factor Kipferl. Through phylogenetic analyses, structure prediction, and in vivo genetics, we identify a single amino acid change within Rhino’s chromodomain, G31D, that does not affect H3K9me2/3 binding but disrupts the interaction between Rhino and Kipferl. Flies carrying the rhinoG31D mutation phenocopy kipferl mutant flies, with Rhino redistributing from piRNA clusters to satellite repeats, causing pronounced changes in the ovarian piRNA profile of rhinoG31D flies. Thus, Rhino’s chromodomain functions as a dual-specificity module, facilitating interactions with both a histone mark and a DNA-binding protein.