Comprehensive functional analysis of the SR protein family of RNA-binding proteins in vivo

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The SR proteins are a family of seven conserved, essential RNA binding proteins, implicated in pre-mRNA splicing, mRNA export, and translation. Because their endogenous RNA targets are unknown, SR protein functions remain mysterious. We established physiological expression of GFP-tagged versions of SR proteins and showed that each associates with pre-mRNA co-transcriptionally and with specific mRNAs after splicing (Sapra et al., 2009). SR proteins exit the nucleus with specific mRNA cargoes. Thus, SR protein interactions with mRNAs at all stages of gene expression can now be detected in vivo. Endogenous pre-mRNA and mRNA targets of SR proteins will be identified in cycling and differentiated neural cells. Importantly, the specific sequences in RNA directly bound by each SR protein in vivo will be determined, mapped to the transcriptome, and compared to genomic patterns of SR protein localization. We will assay the activities of SR proteins and cognate binding sites in alternative splicing, using a “model gene” system. Integration of these datasets will reveal the dynamics and specificity of SR protein RNA targets and provide a framework for understanding how SR proteins regulate gene expression.