Carter et al. combined high-throughput 5’Cap sequencing with standard RNA sequencing to investigate gene expression and transcript diversity in immature (MHC-IIlo) and mature (MHC-IIhi) human mTECs, and demonstrated increased rates of global transcript mis-initiation among the mature mTEC population. In the mature mTEC population, AIRE-dependent, but not FEZF2-dependent, genes showed increased rates for transcript mis-initiation. Differential expression of peripheral splicing factors drove alternative splicing in both mTECs, whereas, during mTEC maturation, specific EREs enriched in long terminal repeat retrotransposons were upregulated.
Contributed by Shishir Pant
ABSTRACT: The induction of central T cell tolerance in the thymus depends on the presentation of peripheral self-epitopes by medullary thymic epithelial cells (mTECs). This promiscuous gene expression (pGE) drives mTEC transcriptomic diversity, with non-canonical transcript initiation, alternative splicing, and expression of endogenous retroelements (EREs) representing important but incompletely understood contributors. Here we map the expression of genome-wide transcripts in immature and mature human mTECs using high-throughput 5' cap and RNA sequencing. Both mTEC populations show high splicing entropy, potentially driven by the expression of peripheral splicing factors. During mTEC maturation, rates of global transcript mis-initiation increase and EREs enriched in long terminal repeat retrotransposons are up-regulated, the latter often found in proximity to differentially expressed genes. As a resource, we provide an interactive public interface for exploring mTEC transcriptomic diversity. Our findings therefore help construct a map of transcriptomic diversity in the healthy human thymus and may ultimately facilitate the identification of those epitopes which contribute to autoimmunity and immune recognition of tumor antigens.