RNA-protein interactomics to read the yeast mRNP code

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We here propose to use mass spectrometry to identify protein binding partners at the level of individual RNA folds and to define an RBP interactome network based on quantitative interactome data. We will use our streamlined RNA-protein interactomics approach to uncover RNA-binding proteins at phylogenetic supported mRNA folds and characterize RNA-dependent mRBP composition in S. cerevisiae. Besides uncovering systematically the functionality of these RNA readers in yeast for a systems perspective, our technique is scalable and widely applicable to any RNA structure and species. It thus can contribute to deciphering the mRNP code also in other model systems.