We have previously developed and optimized methods to map mRNP components and other RNAbinding factors onto the transcriptome in vivo (Schulz et al., Cell 2013; Baejen et al., Mol. Cell 2014). These methods enabled the first global mapping of proteins recognizing pre-mRNA and shortlived RNAs, and demonstrated that RNA recognition cannot be described by standardmethods that are used to describe DNA recognition such as position weight matrices (PWMs). Here we propose an integrated experimental-theoretical approach to contribute to two major goals of the new Schwerpunktprogramm (SPP). First, we will systematically identify cellular binding sitesfor mRNA-binding proteins with the use of PAR-CLIP (photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation), to study formation and function of mRNPs in the budding yeast S. cerevisiae. Second, we will develop new techniques enabling a quantitative description of RNA recognition by cooperative RNA binding of multiple factors that will allow us to predict RNAsequence-binding preferences. The aim of this work is to understand mRNP formation in vivo and to understand the biogenesis and fate of different RNA classes based on their association with cellular factors. The derived technology and bioinformatic tools will be provided to SPP teams.
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