title: Promiscuous mRNA splicing under the control of AIRE in medullary thymic epithelial cells.
abstract: BACKGROUND
  The expression of tissue-restricted antigens (TRAs) in the thymus is required to ensure efficient negative selection of potentially auto-reactive T lymphocytes and avoid autoimmune disease. This promiscuous expression is under the control of the autoimmune regulator (AIRE), a transcription factor expressed in medullary thymic epithelial cells (mTECs). Tissue-specific alternative splicing may also produce TRAs but the extent to which splice isoforms that are restricted to specific tissues are expressed in mTECs is yet to be investigated.
  
  
  RESULTS
  We reanalyzed microarray and RNA-Seq datasets from mouse mTECs and other epithelial and non-epithelial cell types and found that the diversity of splice isoforms in mTECs was greater than in any of the other cell types or tissues studied. We identified tissue-specific isoforms from a panel of mouse tissues and found several examples of such isoforms that are expressed in mTECs. The number of isoforms with restricted expression found in mTECs was significantly higher than for comparable cell types. Furthermore, we found evidence that AIRE influences the increased splicing diversity observed in mTECs as the genes for which tissue restricted isoforms are produced in mTECs were significantly more likely than other genes to be differentially spliced between AIRE knock-out and wild-type samples. Our results suggest that developing T lymphocytes are exposed to diverse tissue-restricted splice isoforms in the thymus and that AIRE has a direct or indirect role in this process, representing a novel aspect of its role in the maintenance of immune self-tolerance.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: School of Mathematics, Statistics and Applied Mathematics and Regenerative Medicine Institute, National University of Ireland, Galway, Ireland.
authors.forename: Peter
authors.initials: P
authors.lastname: Keane
authors.affiliation: School of Mathematics, Statistics and Applied Mathematics and Regenerative Medicine Institute, National University of Ireland, Galway, Ireland.
authors.forename: Rhodri
authors.initials: R
authors.lastname: Ceredig
authors.affiliation: School of Mathematics, Statistics and Applied Mathematics and Regenerative Medicine Institute, National University of Ireland, Galway, Ireland.
authors.forename: Cathal
authors.initials: C
authors.lastname: Seoighe
mesh_terms: D000818:Animals; D002454:Cell Differentiation / Q000235:genetics; D004847:Epithelial Cells / Q000166:cytology / Q000276:immunology / Q000378:metabolism*; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D059014:High-Throughput Nucleotide Sequencing; D051379:Mice; D009928:Organ Specificity; D020033:Protein Isoforms; D012326:RNA Splicing / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism; D013601:T-Lymphocytes / Q000166:cytology / Q000276:immunology* / Q000378:metabolism; D013950:Thymus Gland / Q000166:cytology / Q000378:metabolism*; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism; D000096927:AIRE Protein
chemical_list: D020033:Protein Isoforms; D012333:RNA, Messenger; D014157:Transcription Factors; D000096927:AIRE Protein