Our focus this fall is on RNA : Protein interaction methods and analysis. We are reading papers to learn about classic and novel techniques for identifying which RNA binding proteins interact with an RNA and the position they interact with. We are also interested in learning about bioinformatics methods that predict RNA:protein interactions or recognize conserved sequence or structural motifs.
We are reading:
- Sequence, Structure, and Context Preferences of Human RNA Binding Proteins by Dominguez, D., et al… Yeo, G. W., Graveley, B. R., & Burge, C. B. (2018). Molecular Cell, 70(5), 854-867.e9. https://doi.org/10.1016/j.molcel.2018.05.001
- RBPmap: A web server for mapping binding sites of RNA-binding proteins. Paz, I., Kosti, I., Ares, M., Cline, M., & Mandel-Gutfreund, Y. (2014). Nucleic Acids Research, 42(W1), 1–7. https://doi.org/10.1093/nar/gku406
- Analysis of RNA–protein networks with RNP-MaP defines functional hubs on RNA. Weidmann, C. A., Mustoe, A. M., Jariwala, P. B., Calabrese, J. M., & Weeks, K. M. (2020). Nature Biotechnology. https://doi.org/10.1038/s41587-020-0709-7
- Clusters of mammalian conserved RNA structures in UTRs associate with RBP binding sites. Gadekar VP, Munk AW, Miladi M, Junge A, Backofen R, Seemann SE, Gorodkin J. NAR Genom Bioinform. 2024 Aug 9;6(3):lqae089. doi: 10.1093/nargab/lqae089