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RNA binding proteins (RBPs) regulate the lives of all RNAs from transcription, processing, and function to decay. How RNA–protein interactions change over time and space to support these roles is poorly understood. Towards this end, we sought to determine how two SR proteins—SRSF3 and SRSF7, regulators of pre-mRNA splicing, nuclear export and translation—interact with RNA in different cellular compartments. To do so, we developed Fractionation iCLIP (Fr-iCLIP), in which chromatin, nucleoplasmic and cytoplasmic fractions are prepared from UV-crosslinked cells and then subjected to iCLIP. As expected, SRSF3 and SRSF7 targets were detected in all fractions, with intron, snoRNA and lncRNA interactions enriched in the nucleus. Cytoplasmically-bound mRNAs reflected distinct functional groupings, suggesting coordinated translation regulation. Surprisingly, hundreds of cytoplasmic intron targets …