Role of SR protein modular domains in alternative splicing specificity in vivo

The SR proteins constitute a family of nuclear phosphoproteins which are re quired for constitutive splicing and also influence alternative splicing re gulation. They have a modular structure consisting of one or two RNA recogn ition motifs (RRMs) and a C-terminal domain, rich in arginine and serine re sidues. The functional role of the different domains of SR proteins in cons titutive splicing activity has been extensively studied in vitro; however, their contribution to alternative splicing specificity in vivo has not been clearly established. We sought to address how the modular domains of SR pr oteins contribute to alternative splicing specificity. The activity of a se ries of chimeric proteins consisting of domain swaps between different SR p roteins showed that splice site selection is determined by the nature of th e RRMs and that RRM2 of SF2/ASF has a dominant role and can confer specific ity to a heterologous protein. In contrast, the identity of the RS domain i s not important, as the RS domains are functionally interchangeable. The co ntribution of the RRMs to alternative splicing specificity in vivo suggests that sequence-specific RNA binding by SR proteins is required for this act ivity.