RNA metabolism, RNA processing: This proposal aims to define cellular RNA targets of the essential, highly conserved DEAD-box helicase Ded1p.

• Applicant: Dr. Ulf-Peter Günther
• Subject Area: General Genetics and Functional Genome Biology
• Term: from 2009 to 2012
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 145410858

RNA helicases of the DEAD-box protein family are involved in virtually all aspects of eukaryotic RNA metabolism. Despite recent progress towards understanding the molecular mechanisms of DEAD-box proteins, cellular substrate RNAs have not been identified, and it is unknown which RNA-protein complexes in the cell are targeted by these important enzymes. I propose to identify physiological RNA targets of the essential DEAD-box protein Ded1p from Saccharomyces cerevisiae using a novel experimental approach that combines several complimentary in vivo crosslinking methods, complex purification under denaturing conditions, and deep sequencing. In addition, the binding sites of Ded1p on its RNA targets will be mapped by controlled RNase digestion of crosslinked RNAs and subsequent deep sequencing. The proposed work will provide the first comprehensive definition of cellular RNA binding sites for a DEAD-box protein and thus offer unique and unprecedented insights into the biological function of these essential proteins. Equally important, the developed methodology will enable the definition of RNA targets for other cellular RNA helicases, which is pivotal for understanding the cellular roles of these critical enzymes.

• DFG Programme: Research Fellowships
• International Connection: USA
• Host: Dr. Eckhard Jankowsky