Structural studies on mRNA recognition by FMRP and TDP-43, two RNA-binding proteins associated with neuronal diseases
Final Report Abstract
The deregulation of posttranscriptional regulatory networks by genetic mutation, deletion or overexpression of RNA-binding proteins results in disease, yet their target RNAs and their modes of regulation are largely unknown. Many neurodegenerative conditions are caused by altered RBP expression that perturbs post-transcriptional regulatory networks. Examples include Fragile-X-Syndrome (FXS) and amyotrophic lateral sclerosis (ALS). This research project was aimed to understand the recognition of mRNA targets to deduce the regulatory principles of two disease-associated RBPs, one of which (FMRP) is associated with the FXS and particular types of autism, whereas mutations in the other (TDP-43) are associated with ALS. Molecular RNA targets of these RBPs were identified using PAR-CLIP (photoactivatable ribonucleotide crosslinking and immunoprecipitation) in combination with high-throughput sequencing. This allowed an efficient identification of cellular RNA targets and the determination of RNA recognition elements from their consensus sequences. The RBPs were analyzed in the presence and absence of their biologically relevant RNA targets as well as further interaction partners using biophysical and structural-biology methods. This approach went beyond analyses of short RNA fragments with isolated RNA-binding domains. Results on the molecular structure and folding states of the RBPs in the presence and absence of their ligands allowed the generation of hypotheses of their molecular function and regulation, which were be investigated using "in-vitro" models and living cells. An understanding of RBPs at the molecular level as well as in a cellular environment may contribute to the development of specific pharmacological interventions.
Publications
- (2011). RNA single strands bind to a conserved surface of the major cold shock protein in crystals and solution. RNA 18: 65-76
Sachs, R., Max, K. E. A., Heinemann, U., Balbach, J.
- (2013). Identification of mRNAs bound and regulated by human LIN28 proteins and molecular requirements for RNA recognition. RNA 19:613-626
Hafner, M., Max, K. E. A., Bandaru, P., Morozov, P., Gerstberger, S., Molina H., Brown, M., Tuschl, T.
- (2014). Identification of the RNA recognition element of the RBPMS family of RNA-binding proteins and their transcriptome-wide mRNA targets. RNA 20:1090-1102
Farazi, T. A., Leonhardt, C. S., Mukherjee, N., Mihailovic A., Li S., Max K. E. A., Meyer C., Yamaji M., Cekan P., Jacobs N. C., Gerstberger S., Bognanni C., Larsson E., Ohler U., Tuschl T.
(See online at https://doi.org/10.1261/rna.045005.114)
