RBPbase v0.1.8 alpha

A COMPREHENSIVE DATABASE OF EUKARYOTIC RNA-BINDING PROTEINS (RBP) WITH THEIR RBP ANNOTATIONS


Welcome to RBPbase, a database that integrates high-throughput RNA-binding protein (RBP) detection studies. For context, we recommend our review on RNA-binding proteins [1], and the technical descriptions of RNA interactome capture (RIC) [2,3,4], a mass spectrometry (MS) based protocol. The latest refinements of this protocol include enhanced RIC (eRIC) [5] and many others which can be found under tab 'Studies'.



We accelerated the release of this first public version in response to the SARS-CoV-2 crisis. We will continuously introduce refinements and welcome feedback. While no SARS-CoV-2 RNA interactome is currently available, SARS-CoV-2 proteomics are already underway. Since SARS-CoV-2 is an RNA virus, it is expected to intensively use host RBPs for its replicative cycle. We hope that RBPbase will help to identify relevant host proteins as RBPs, which could be helpful for understanding viral biology and ultimately the design of therapeutic strategies. To support SARS-CoV-2 research the database also provides annotations for 332 experimentally validated SARS-CoV-2-human protein-protein interactions (PPIs) [6].



References:
[1] Hentze, M.W., Castello, A., Schwarzl, T. and Preiss, T., 2018. A brave new world of RNA-binding proteins. Nature Reviews Molecular Cell Biology, 19(5), p.327. https://doi.org/10.1038/nrm.2017.130
[2] Baltz, A.G., Munschauer, M., Schwanh├Ąusser, B., Vasile, A., Murakawa, Y., Schueler, M., Youngs, N., Penfold-Brown, D., Drew, K., Milek, M. and Wyler, E., 2012. The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Molecular cell, 46(5), pp.674-690. https://doi.org/10.1016/j.molcel.2012.05.021
[3] Castello, A., Fischer, B., Eichelbaum, K., Horos, R., Beckmann, B.M., Strein, C., Davey, N.E., Humphreys, D.T., Preiss, T., Steinmetz, L.M. and Krijgsveld, J., 2012. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Cell, 149(6), pp.1393-1406. https://doi.org/10.1016/j.cell.2012.04.031
[4] Castello, A., Horos, R., Strein, C., Fischer, B., Eichelbaum, K., Steinmetz, L.M., Krijgsveld, J. and Hentze, M.W., 2013. System-wide identification of RNA-binding proteins by interactome capture. Nature protocols, 8(3), p.491. https://doi.org/10.1038/nprot.2013.020
[5] Perez-Perri, J.I., Rogell, B., Schwarzl, T., Stein, F., Zhou, Y., Rettel, M., Brosig, A. and Hentze, M.W., 2018. Discovery of RNA-binding proteins and characterization of their dynamic responses by enhanced RNA interactome capture. Nature communications, 9(1), pp.1-13. https://doi.org/10.1038/s41467-018-06557-8
[6] Gordon, D.E., Jang, G.M., Bouhaddou, M., Xu, J., Obernier, K., O'meara, M.J., Guo, J.Z., Swaney, D.L., Tummino, T.A., Huttenhain, R. and Kaake, R.M., 2020. A SARS-CoV-2-human protein-protein interaction map reveals drug targets and potential drug-repurposing. BioRxiv. https://doi.org/10.1101/2020.03.22.002386

Show RBPs only
Somatic Disease Mutations
SARS-CoV-2 PPI
RBPs virus infection

About

Impressum


This database is hosted and maintained by

Hentze Group
European Molecular Biology Laboratory (EMBL)
Thomas Schwarzl, PhD, Staff Scientist in Hentze and Huber Group
Meyerhofstra├če 1
69117 Heidelberg.

Please contact biohentze@embl.de for support or inqueries.


Versions

Annotations and database


The identifiers are based on Ensembl ID 92, Homology mapping was done with EggNog database[1].


[1] Jensen, L.J., Julien, P., Kuhn, M., von Mering, C., Muller, J., Doerks, T. and Bork, P., 2007. eggNOG: automated construction and annotation of orthologous groups of genes. Nucleic acids research, 36(suppl_1), pp.D250-D254. https://doi.org/10.1093/nar/gkm796

Acknowledgements

Thank you very much


Eva Schitter for the work on homology mapping during an intership at the Hentze lab.


Wolfgang Huber for advice and feedback.


Josep Manel Andres Moscardo and EMBL IT Services for hosting the Shiny App and EMBL Bio-IT for hosting Gitlab services.