ArticleGenome research2014
Population and single-cell genomics reveal the Aire dependency, relief from Polycomb silencing, and distribution of self-antigen expression in thymic epithelia.
Article in Genome research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 227 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
227 citing papers in PubMed, 332 citations in OpenAlex.
- Trial
- Central T cell tolerance from sparse peptide sampling.Science advances · 2026Article
- Ly6d expression delineates two putative postnatal thymus epithelial progenitor cells that are differentially affected by aging.Science advances · 2026Article
- FGF21 induced by endoplasmic reticulum stress maintains medullary thymic epithelial cell function and central immune tolerance.Science advances · 2026Article
- The autoimmune regulator (AIRE) is a target of the E3-Ubiquitin ligase Seven-in-absentia homolog 1 (SIAH1).Apoptosis : an international journal on programmed cell death · 2026Article
- What Do We Know About Immune System Aging from Human and Animal Studies?International journal of molecular sciences · 2026Review
- Thymic alveolar type 2 epithelial mimetic cells revealed by RUNX1 deficiency.Nature immunology · 2026Article
- ZFP36L1 and ZFP36L2 cooperatively regulate thymic epithelial cell function to prevent early-onset thymic involution.Cell death and differentiation · 2026Article
- Foxp1 controls Fezf2-dependent gene expression, mimetic mTEC diversity, and thymic central tolerance.Journal of immunology (Baltimore, Md. : 1950) · 2026Article
- Runx3 instructs AireJournal of autoimmunity · 2026Article
- Multimerizing transcription factors FOXP3 and AIRE as chromatin architectural regulators.Nature immunology · 2026Review
- KLF2 controls thymic epithelial cell homeostasis, impacting regulatory T cell development and immune tolerance.iScience · 2026Article
- Neonatal Thymic Dynamics Influence Autoimmune Pathology by Shaping the Suppressive Potential of Regulatory T Cells.The American journal of pathology · 2026Article
- Thymic epithelial tumors at the crossroads of immunity, autoimmunity, and immunotherapy.Cancer immunology, immunotherapy : CII · 2026Review
- Claudin 1-mediated positioning of DC1 to mTECs is essential for maintenance of central tolerance.The Journal of experimental medicine · 2026Article
- Fezf2 regulates differentiation of Aire-expressing and post-Aire mimetic epithelial populations maintaining thymic homeostasis.bioRxiv : the preprint server for biology · 2026Article
- Understanding immune checkpoint inhibitors-related myocarditis: Mechanisms and targeted therapeutic pathways.Theranostics · 2026Review
- AIRE transcriptional condensates in central tolerance: a multiscale mechanistic perspective.Frontiers in immunology · 2026Review
- Unexpected heterogeneity and tissue-specific properties of the thymic hematopoietic antigen-presenting cell network.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Article
167 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 3 institutions in 3 countries.
Funding
Abstract
Promiscuous gene expression (PGE) by thymic epithelial cells (TEC) is essential for generating a diverse T cell antigen receptor repertoire tolerant to self-antigens, and thus for avoiding autoimmunity. Nevertheless, the extent and nature of this unusual expression program within TEC populations and single cells are unknown. Using deep transcriptome sequencing of carefully identified mouse TEC subpopulations, we discovered a program of PGE that is common between medullary (m) and cortical TEC, further elaborated in mTEC, and completed in mature mTEC expressing the autoimmune regulator gene (Aire). TEC populations are capable of expressing up to 19,293 protein-coding genes, the highest number of genes known to be expressed in any cell type. Remarkably, in mouse mTEC, Aire expression alone positively regulates 3980 tissue-restricted genes. Notably, the tissue specificities of these genes include known targets of autoimmunity in human AIRE deficiency. Led by the observation that genes induced by Aire expression are generally characterized by a repressive chromatin state in somatic tissues, we found these genes to be strongly associated with H3K27me3 marks in mTEC. Our findings are consistent with AIRE targeting and inducing the promiscuous expression of genes previously epigenetically silenced by Polycomb group proteins. Comparison of the transcriptomes of 174 single mTEC indicates that genes induced by Aire expression are transcribed stochastically at low cell frequency. Furthermore, when present, Aire expression-dependent transcript levels were 16-fold higher, on average, in individual TEC than in the mTEC population.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.