Population and single cell genomics reveal the Aire-dependency, relief from Polycomb silencing and distribution of self-antigen expression in thymic epithelia
- Stephen N Sansom1,5,
- Noriko Shikama2,
- Saule Zhanybekova2,
- Gretel Nusspaumer2,
- Iain C Macaulay3,
- Mary E Deadman1,
- Andreas Heger1,
- Chris P Ponting1 and
- Georg A Holländer4
- 1 University of Oxford;
- 2 University of Basel;
- 3 Wellcome Trust Sanger Institute;
- 4 University of Oxford & University of Basel
- ↵* Corresponding author; email: stephen.sansom{at}kennedy.ox.ac.uk
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 discover a program of PGE that is common between medullary (m) and cortical TEC, further elaborated in mature 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 alone positively regulates 3980 genes which are otherwise tissue-restricted in expression. Notably, the tissue specificities of these genes include known targets of autoimmunity in human AIRE deficiency. Led by an observation that Aire-induced genes 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 Aire-induced genes are expressed stochastically at low cell frequency. Furthermore, when expressed, Aire-dependent transcript levels were 16-fold higher, on average, in individual TEC than in the mTEC population.
- Received December 22, 2013.
- Accepted September 12, 2014.
- Published by Cold Spring Harbor Laboratory Press
This manuscript is Open Access.
This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International license), as described at http://creativecommons.org/licenses/by-nc/4.0/.
