In vitro iCLIP-based modeling uncovers how the splicing factor U2AF2 relies on regulation by cofactors

Cofactors change U2AF2^RRM12 binding in vitro. (A) Different patterns of U2AF2 regulation by cofactors can be observed in vitro. Heat map showing log₂FC of normalized U2AF2^RRM12 read counts upon addition of cofactors (U2AF2^RRM12 + cofactor/U2AF2^RRM12). In vitro transcripts indicated above. Only binding sites with |log₂FC| > 2 in at least one cofactor experiment are shown. (B) Several cofactors significantly change U2AF2^RRM12 binding. Bar plot showing log₂FC upon cofactor addition as in A for sites with no cofactor motif (white) as well as sites with cofactor motif and not regulated (gray, −0.5 < z-score < 0.5), stabilized in vivo (blue, z-score > 1), or cleared in vivo (orange, z-score < −1). Data were scaled such that log₂FC of sites without cofactor motif are centered around zero. Added cofactor concentrations are indicated in each panel. Dots indicate individual data points for n < 50. Adjusted P-values are given for all groups with false discovery rate (FDR) < 10% (two-sided Student's t-test, Benjamini–Hochberg correction, compared to binding sites without cofactor motif).