The pioneer transcription factors Foxa1 and Foxa2 regulate alternative RNA splicing during thymocyte positive selection

Development. 2021 Aug 1;148(15):dev199754. doi: 10.1242/dev.199754. Epub 2021 Jul 29.

Abstract

During positive selection at the transition from CD4+CD8+ double-positive (DP) to single-positive (SP) thymocyte, TCR signalling results in appropriate MHC restriction and signals for survival and progression. 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 naïve 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 >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.

Keywords: Foxa1; Foxa2; Mouse; Positive selection; RNA splicing; T-cell development; Thymus.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alternative Splicing / genetics*
  • Animals
  • Exons / genetics
  • Hepatocyte Nuclear Factor 3-alpha / genetics*
  • Hepatocyte Nuclear Factor 3-beta / genetics*
  • Mice
  • Mice, Inbred C57BL
  • Mice, Transgenic
  • RNA Splicing / genetics*
  • RNA Splicing Factors / genetics
  • T-Lymphocytes / physiology
  • Thymocytes / physiology*
  • Thymus Gland / physiology

Substances

  • Foxa1 protein, mouse
  • Foxa2 protein, mouse
  • Hepatocyte Nuclear Factor 3-alpha
  • RNA Splicing Factors
  • Hepatocyte Nuclear Factor 3-beta