Mayr C, Bartel DP. 2009. Widespread shortening of 3' UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells. *Cell* **138**:673-684. DOI: https://doi.org/10.1016/j.cell.2009.06.016, PMID: 19703394

Millevoi S, Vagner S. 2010. Molecular mechanisms of eukaryotic pre-mRNA 3' end processing regulation. *Nucleic Acids Research* **38**:2757-2774. DOI: https://doi.org/10.1093/nar/gkp1176, PMID: 20044349

Mizuochi T, Kasai M, Kokuho T, Kakiuchi T, Hirokawa K. 1992. Medullary but not cortical thymic epithelial cells present soluble antigens to helper T cells. *The Journal of Experimental Medicine* **175**:1601-1605. DOI: https://doi.org/10.1084/jem.175.6.1601, PMID: 1534114

Nagamine K, Peterson P, Scott HS, Kudoh J, Minoshima S, Heino M, Krohn KJ, Lalioti MD, Mullis PE, Antonarakis SE, Kawasaki K, Asakawa S, Ito F, Shimizu N. 1997. Positional cloning of the APECED gene. *Nature Genetics* **17**:393-398. DOI: https://doi.org/10.1038/ng1297-393, PMID: 9398839

Oliveira EH, Macedo C, Collares CV, Freitas AC, Donate PB, Sakamoto-Hojo ET, Donadi EA, Passos GA. 2016. Aire downregulation is associated with changes in the posttranscriptional control of peripheral tissue antigens in medullary thymic epithelial cells. *Frontiers in Immunology* **7**:526. DOI: https://doi.org/10.3389/fimmu.2016.00526, PMID: 27933063

Pan JB, Hu SC, Shi D, Cai MC, Li YB, Zou Q, Ji ZL. 2013. PaGenBase: a pattern gene database for the global and dynamic understanding of gene function. *PLOS ONE* **8**:e08747. DOI: https://doi.org/10.1371/journal.pone.0080747, PMID: 24312499

Passos GA, Mendes-da-Cruz DA, Oliveira EH. 2015. The thymic orchestration involving aire, miRNAs, and Cell-Cell interactions during the induction of central tolerance. *Frontiers in Immunology* **6**:352. DOI: https://doi.org/10.3389/fimmu.2015.00352, PMID: 26236310

Peterson P, Pitkänen J, Sillanpää N, Krohn K. 2004. Autoimmune polyendocrinopathy candidiasis ectodermal dystrophy (APECED): a model disease to study molecular aspects of endocrine autoimmunity. *Clinical and Experimental Immunology* **135**:348-357. DOI: https://doi.org/10.1111/j.1365-2249.2004.02384.x, PMID: 15008965

Quinlan AR, Hall IM. 2010. BEDTools: a flexible suite of utilities for comparing genomic features. *Bioinformatics* **26**:841-842. DOI: https://doi.org/10.1093/bioinformatics/btq033, PMID: 20110278

Sansom SN, Shikama-Dorn N, Zhanybekova S, Nusspaumer G, Macaulay IC, Deadman ME, Heger A, Ponting CP, Holländer GA. 2014. Population and single-cell genomics reveal the aire dependency, relief from Polycomb silencing, and distribution of self-antigen expression in thymic epithelia. *Genome Research* **24**:1918-1931. DOI: https://doi.org/10.1101/gr.171645.113, PMID: 25224068

Shen Y, Yue F, McCleary DF, Ye Z, Edsall L, Kuan S, Wagner U, Dixon J, Lee L, Lobanenkov VV, Ren B. 2012. A map of the cis-regulatory sequences in the mouse genome. *Nature* **488**:116-120. DOI: https://doi.org/10.1038/nature11243, PMID: 22763441

Shi Y, Di Giammartino DC, Taylor D, Sarkeshik A, Rice WJ, Yates JR, Frank J, Manley JL. 2009. Molecular architecture of the human pre-mRNA 3' processing complex. *Molecular Cell* **33**:365-376. DOI: https://doi.org/10.1016/j.molcel.2008.12.028, PMID: 19217410

Shin H, Liu T, Manrai AK, Liu XS. 2009. CEAS: cis-regulatory element annotation system. *Bioinformatics* **25**:2605-2606. DOI: https://doi.org/10.1093/bioinformatics/btp479, PMID: 19689956

Sobell HM. 1985. Actinomycin and DNA transcription. *PNAS* **82**:5328-5331. DOI: https://doi.org/10.1073/pnas.82.16.5328, PMID: 2410919

Spies N, Burge CB, Bartel DP. 2013. 3' UTR-isiform choice has limited influence on the stability and translational efficiency of most mRNAs in mouse fibroblasts. *Genome Research* **23**:2078-2090. DOI: https://doi.org/10.1101/gr.156919.113, PMID: 24072873

Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP. 2005. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. *PNAS* **102**:15545-15550. DOI: https://doi.org/10.1073/pnas.0506580102, PMID: 16199517

Tian B, Manley JL. 2013. Alternative cleavage and polyadenylation: the long and short of it. *Trends in Biochemical Sciences* **38**:312-320. DOI: https://doi.org/10.1016/j.tibs.2013.03.005

Ucar O, Tykocinski L-O, Dooley J, Liston A, Kyewski B. 2013. An evolutionarily conserved mutual interdependence between aire and microRNAs in promiscuous gene expression. *European Journal of Immunology* **43**:1769-1778. DOI: https://doi.org/10.1002/eji.201343343

van den Berghe V, Stappers E, Vandesande B. Dimidschstein J, Kroes R, Francis A, Conidi A, Lesage F, Dries R, Cazzola S, Berx G, Kessaris N, Vanderhaeghen P, van Ijcken W, Grosveld FG, Goossens S, Haigh JJ, Fishell G, Goffinet A, Aerts S, et al. 2013. Directed migration of cortical interneurons depends on the cell-autonomous action of Sip1. *Neuron* **77**:70-82. DOI: https://doi.org/10.1016/j.neuron.2012.11.009, PMID: 23312517

Vlasova IA, Tahoe NM, Fan D, Larsson O, Rattenbacher B, Sternjohn JR, Vasdewani J, Karypis G, Reilly CS, Bitterman PB, Bohjanen PR. 2008. Conserved GU-rich elements mediate mRNA decay by binding to CUG-binding protein 1. *Molecular Cell* **29**:263-270. DOI: https://doi.org/10.1016/j.molcel.2007.11.024, PMID: 18243120

Warren BL, Vialou VF, Iñiguez SD, Alcantara LF, Wright KN, Feng J, Kennedy PJ, Laplant Q, Shen L, Nestler EJ, Bolaños-Guzmán CA. 2013. Neurobiological sequelae of witnessing stressful events in adult mice. *Biological Psychiatry* **73**:7-14. DOI: https://doi.org/10.1016/j.biopsych.2012.06.006, PMID: 22795644