Deciphering the molecular code of protein-RNA binding during mRNA localisation

• Applicant: Dr. Katharina Zarnack
• Subject Area: General Genetics and Functional Genome Biology ; Bioinformatics and Theoretical Biology
• Term: from 2015 to 2020
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 270067186

mRNA localisation and local translation are regulated by RNA-binding proteins (RBPs) that constitute critical regulators of eukaryotic gene expression. Target mRNAs are recognised via cis-acting elements in the RNA sequence, so-called zipcodes or localisation elements, which are composed of characteristic sequence motifs and/or structural elements. RBPs recruit the target mRNAs into large transport particles which most often move actively along cytoskeletal tracks in the cytoplasm. Recently, evidence is accumulating that co-trafficking of mRNAs with membrane structures is another frequently occurring mode of intracellular mRNA transport. In order to address the prevalence and possible functions of this new transport route, we will perform a comprehensive survey of membrane-associated RBPs in fungi and mammals in collaboration with several groups of the FOR2333.Over the last years, new ribonomic techniques have been introduced that allow to study RBP binding and its regulatory outcome on a genomic scale, including UV crosslinking and immunoprecipitation (CLIP) and related methods to map RBP binding sites in vivo. However, the analysis and interpretation of these data is still in its infancy. In order to overcome these limitations and reliably map and quantify RBP binding, we will benchmark existing tools based on publicly available iCLIP datasets for different RBPs. Moreover, we will develop robust quantification strategies that correct for differences in transcript abundance, among others. The resulting RBP binding sites will be characterised in terms of motif occurrence, binding site conformations and RNA secondary structure formation. By interrelating these features we will obtain new insights into the molecular code that determines RBP binding. In collaboration with several groups of the FOR2333, we will exploit the established analysis workflows to learn more about the RNA binding mode of the She mRNA transport complex in yeast, the target recognition of the translational regulator Pumilio2 in mammalian neurons and the functional impact of the exon-junction complex on mRNA localisation in fruit flies.

• DFG Programme: Research Units
• Subproject of: FOR 2333: Macromolecular Complexes in mRNA translocation