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We show that the pioneer transcription factors Foxa1 and Foxa2 are required to regulate RNA splicing during positive selection of mouse T cells and that Foxa1 and Foxa2 have overlapping\/compensatory roles. Conditional deletion of both Foxa1 and Foxa2 from DP thymocytes reduced positive selection and development of CD4SP, CD8SP and peripheral na\u00efve CD4+ T cells. Foxa1 and Foxa2 regulated the expression of many genes encoding splicing factors and regulators, including Mbnl1, H1f0, Sf3b1, Hnrnpa1, Rnpc3, Prpf4b, Prpf40b and Snrpd3. Within the positively selecting CD69+DP cells, alternative RNA splicing was dysregulated in the double Foxa1\/Foxa2 conditional knockout, leading to &amp;gt;850 differentially used exons. Many genes important for this stage of T-cell development (Ikzf1-3, Ptprc, Stat5a, Stat5b, Cd28, Tcf7) and splicing factors (Hnrnpab, Hnrnpa2b1, Hnrnpu, Hnrnpul1, Prpf8) showed multiple differentially used exons. Thus, Foxa1 and Foxa2 are required during positive selection to regulate alternative splicing of genes essential for T-cell development, and, by also regulating splicing of splicing factors, they exert widespread control of alternative splicing.<\/jats:p>","DOI":"10.1242\/dev.199754","type":"journal-article","created":{"date-parts":[[2021,7,2]],"date-time":"2021-07-02T11:36:25Z","timestamp":1625225785000},"source":"Crossref","is-referenced-by-count":21,"title":["The pioneer transcription factors Foxa1 and Foxa2 regulate alternative RNA splicing during thymocyte positive selection"],"prefix":"10.1242","volume":"148","author":[{"given":"Ching-In","family":"Lau","sequence":"first","affiliation":[{"name":"UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7040-8528","authenticated-orcid":false,"given":"Jasmine","family":"Rowell","sequence":"additional","affiliation":[{"name":"UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Diana C.","family":"Yanez","sequence":"additional","affiliation":[{"name":"UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anisha","family":"Solanki","sequence":"additional","affiliation":[{"name":"UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susan","family":"Ross","sequence":"additional","affiliation":[{"name":"UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Masahiro","family":"Ono","sequence":"additional","affiliation":[{"name":"Department of Life Sciences, Imperial College London, London SW7 2AZ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8973-4021","authenticated-orcid":false,"given":"Tessa","family":"Crompton","sequence":"additional","affiliation":[{"name":"UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"237","published-online":{"date-parts":[[2021,7,29]]},"reference":[{"key":"2021072911592712300_DEV199754C1","doi-asserted-by":"publisher","first-page":"2008","DOI":"10.1101\/gr.133744.111","article-title":"Detecting differential usage of exons from RNA-seq data","volume":"22","author":"Anders","year":"2012","journal-title":"Genome Res."},{"key":"2021072911592712300_DEV199754C2","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1093\/bioinformatics\/btu638","article-title":"HTSeq--a Python framework to work with high-throughput sequencing data","volume":"31","author":"Anders","year":"2015","journal-title":"Bioinformatics"},{"key":"2021072911592712300_DEV199754C3","doi-asserted-by":"publisher","first-page":"5464","DOI":"10.4049\/jimmunol.166.9.5464","article-title":"Fine tuning of TCR signaling by CD5","volume":"166","author":"Azzam","year":"2001","journal-title":"J. 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