U2AF2 binds IL7R exon 6 ectopically and represses its inclusion

Interleukin 7 receptor α-chain is crucial for the development and maintenance of T cells and genetically associated with autoimmune disorders including multiple sclerosis (MS). Exon 6 of IL7R encodes for its transmembrane domain and regulated by alternative splicing (AS): Inclusion or skipping of IL7R exon 6 results in membrane-bound or soluble IL7R isoforms, respectively. We previously identified SNP rs6897932 in IL7R exon 6, associated with MS risk, and showed that the risk allele (C) results in increased exon skipping and elevated sIL7R. Elevated levels of sIL7R have been shown to exacerbate the disease in the experimental autoimmune encephalomyelitis mouse model of MS. Here we report two mechanisms by which IL7R exon 6 is controlled. A competition between PTBP1 and U2AF2 at the polypyrimidine tract (PPT) of intron 5, and an unexpected U2AF2-mediated assembly of splicing factors in the exon. We noted the presence of a branchpoint sequence (BPS) (TACTAAT or TACTAAC) within exon 6, which is stronger with the C allele. Importantly, the BPS is followed by a PPT and we conjectured that silencing could be mediated by binding of U2AF2 to that tract. Here, we show that evolutionary conservation of the exonic PPT correlates well with the degree of AS of exon 6 in two nonhuman primate species and that U2AF2 binding to this PPT recruits U2 snRNP components to the exon. These observations provide the first explanation for the stronger silencing of IL7R exon 6 with the disease-associated C allele at rs6897932.