Phone: 0043 1 4277 79730
Research Group: http://www.imp.ac.at/research/biology-computation-and-engineering/stark-group/
Institution: Research Institute of Molecular Pathology (IMP)
Full member of the DoktortsKolleg RNA Biology since 2014
DK PhD Student:
M. Mamduh A. ZABIDI
Joint research project J. Brennecke and A. Stark:
We propose to perform an unbiased study of RNA-abundance and post-transcriptional regulation in the female Drosophila germ line. Drosophila oogenesis serves as a paradigm for regulation of gene expression at the RNA-level, as all 3 known small RNA pathways (miRNAs, siRNAs, PiRNAs) are employed and it is the key system in which control of RNA localization, translation and transport have been established and are actively studied.
Specifically, we will establish and employ ribosome foot-printing (Ingolia et al. 2009) to determine ribosome occupancy and translation rates of mRNAs and RNA-PAR-CLIP (Hafner et al, 2010) to identify the specific target RNAs of three key protein factors involved in post-transcriptional regulation (Pumilio, Staufen, and Argonaute 1). We will couple these genom-wide approaches to bioninformatics analyses established in our or the Hofacker groups to determine the cis-regulatory motifs of RNAs at the level of sequence and secondary structure. We anticipate gaining significant insight into the post-transcriptional control of RNA fate in a complex in vivo context.
In a broader perspective, both technologies will proof extremely useful for the scientific progress within the Brennecke/Stark labs, which are focusing on small RNAs and cis-regulatory motifs. Finally, we believe that multiple groups within this SFB (e.g. Kiebler, Dorner, Mochizuki, Martinez) and a number of labs at the Vienna Biocenter Campus will benefit strongly from the establishment of the two technologies.