High-Resolution Profiling of Protein-RNA Interactions

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This book exemplifies how innovative experimentation and technology, alongside computational data analysis, enhance our understanding of biological entities from a systems perspective. It details the investigation of a single RNA-binding protein and its interaction sites, leading to the creation of the groundbreaking ‘protein occupancy profiling’ technology. This method uniquely captures the mRNA sequence space engaged by various expressed RNA binders. When applied to eukaryotic cells, it uncovered that extensive regions in 3’ UTRs are contacted by RBPs, with evidence of evolutionary conservation and negative selection at protein-RNA contact sites, indicating their functional significance. The comparative analysis of RBP-bound sequences could reveal potential cis-acting RNA elements without prior knowledge of the regulators involved. Dr. Munschauer offers a thorough introduction to post-transcriptional gene regulation, explores cutting-edge technologies, and synthesizes findings from multiple journal articles into a coherent narrative at the forefront of systems biology in life sciences. This thesis, submitted to the Department of Biology, Chemistry and Pharmacy at Freie Universität Berlin, was recognized as outstanding by the Berlin Institute for Medical Systems Biology at the Max-Delbrueck Center for Molecular Medicine, Germany.