Population and single-cell genomics reveal the Aire dependency, relief from Polycomb silencing, and distribution of self-antigen expression in thymic epithelia

Stephen N Sansom, Noriko Shikama-Dorn, Saule Zhanybekova, Gretel Nusspaumer, Iain C Macaulay, Mary E Deadman, Andreas Heger, Chris P Ponting, Georg A Holländer

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish
Pages (from-to)1918-31
Number of pages14
JournalGenome Research
Issue number12
Publication statusPublished - 15 Sep 2014


  • Acetylation
  • Animals
  • Autoantigens
  • Chromatin
  • Cluster Analysis
  • Computational Biology
  • Epithelial Cells
  • Gene Expression
  • Gene Expression Profiling
  • Gene Expression Regulation
  • Gene Order
  • Gene Silencing
  • Gene Targeting
  • Genetic Loci
  • Genetic Vectors
  • Genomics
  • Histones
  • Mice
  • Mice, Transgenic
  • Organ Specificity
  • Polycomb-Group Proteins
  • Signal Transduction
  • Single-Cell Analysis
  • Thymus Gland
  • Transcription Factors
  • Transcriptome


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