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Genes associated with increased susceptibility to multiple sclerosis (MS) have been identified, but their functions are incompletely understood. One of these genes codes for the RNA helicase DExD/H-Box Polypeptide 39B (DDX39B), which shows genetic and functional epistasis with interleukin-7 receptor-α gene ( IL7R ) in MS-risk. Based on evolutionary and functional arguments, we postulated that DDX39B enhances immune tolerance thereby decreasing MS risk. Consistent with such a role we show that DDX39B controls the expression of many MS susceptibility genes and important immune-related genes. Among these we identified Forkhead Box P3 ( FOXP3 ), which codes for the master transcriptional factor in CD4 + /CD25 + T regulatory cells. DDX39B knockdown led to loss of immune-regulatory and gain of immune-effector expression signatures. Splicing of FOXP3 introns, which belong to a previously unrecognized type of introns with C-rich polypyrimidine tracts, was exquisitely sensitive to DDX39B levels. Given the importance of FOXP3 in autoimmunity, this work cements DDX39B as an important guardian of immune tolerance., Competing Interests: MH, CN, GS, LW, AA, VJ, XY, SW, FB, SG, DK, WF, SB No competing interests declared, GG, MG I acknowledge that I have significant ownership in Autoimmunity Biologic Solutions, Inc (Galveston, TX), which is commercializing therapies that target the IL7R pathway in autoimmune diseases. While I do not believe this represents a conflict of interest it can lead to the perception of said conflict, (© 2023, Hirano, Galarza-Muñoz et al.)