11 Aug

Analysis of circRNPs

Are circular RNAs (circRNAs) translated? It is very intriguing to speculate that (at least some) circRNAs might encode functional peptides. So far however, evidence in support of this theory is weak. One might hypothesize that by non-canonical initiation once in a while a ribosome might indeed translate an open reading frame encoded by circular RNA, whether this yields significant amounts of a functional protein still remains to be demonstrated.

In a collaborative effort with the Bindereif lab at the Justus-Liebig-University of Giessen, we have analyzed the sedimentation of circRNAs in sucrose gradients.  If circRNAs are indeed translated this could be revealed by a change of sedimentation behavior after treatment with a drug that releases elongating ribosomes from RNAs (Puromycin). In our experiments however, no significant change in sedimentation behavior of selected abundant circRNPs from HeLa cells could be observed, suggesting that these circRNAs are not (or at best only weakly) translated.

Scientific reportsCircRNAs do however associate with proteins to form ribonucleoproteins (RNPs). In our recent publication ‘CircRNA-protein complexes: IMP3 protein component defines subfamily of circRNPs’ (published in Scientific Reports) we demonstrate that in HeLa cells, circRNAs form distinct, large RNPs. Moreover, we identify the RNA-binding protein and tumor marker IMP3 (IGF2BP3) as a protein component of numerous circRNPs.

(Picture taken from Schneider et al., 2016, Scientific Reports 6, 31313, doi:10.1038/srep31313, CC 4.0)

 

 

31 May

Bioinformatics Course at the University of Regensburg

Bioinformatikkurs

 

From October 10th to 14th 2016, a methods course on ‘Analysis of NextGen RNA-Seq data for expression profiling and protein binding RNAs‘ will take place here in Regensburg. Insightful lectures will be deliverd by reknown experts in the field, including (in alphabetical order) Simon Anders (FIMM Helsinki), Markus Hafner (NIAMS/NIH Bethesda), Steve Hoffman (University of Leipzig), Stefan Kirsch (Fraunhofer  ITEM, Regensburg), Charlotte Soneson (University of Zurich), Rainer Spang (University of Regensburg), Nicholas Strieder (University of Regensburg), and Grischa Toedt (EMBL Heidelberg). After the lectures, there will be ample time for hands-on training allowing the participants to gain some practical experience with the latest computational approaches. If you are interested in participating, please register before July 13th.

The course is generously supported by the Graduate Research Academy RNA Biology of the Collaborate Research Center SFB960 ‘Ribosome formation: principles of RNP biogenesis and control of their function’.

31 Mar

Review article: The expanding universe of ribonucleoproteins

Soon a special issue with focus on ‘RNA biology in physiology and disease’ will be published by the European Journal of Physiology (Pflügers Archiv). Together with our colleagues Benedikt Beckmann (IRI for the Life Sciences, Humboldt University Berlin) and Alfredo Castello (University of Oxford) we have contributed a review article entitled: The expanding universe of ribonucleoproteins – of novel RNA-binding proteins and unconventional interactions.

We focus on the recent advances in the identification of novel RNA-binding proteins (RBPs) and the unexpected finding that many of the novel RBPs do not contain identifiable RNA-binding domains (RBDs), raising the question of how they interact with RNA. It is surprising that despite the many functions that have been attributed to RNA, our understanding of ribonucleoproteins (RNPs) is still mostly governed by a rather protein-centric view, leading to the idea that proteins have evolved to bind to and regulate RNA and not vice versa. However, RNPs formed by an RNA-driven interaction mechanism (‘RNA-determined RNPs’) are abundant and offer an alternative explanation for the surprising lack of ‘classical’ RBDs in many RNA-interacting proteins (which we discuss in detail in the review article).

HCV-on-40SHCV IRES bound to a 40S ribosomal subunit, structure based on Yamamoto et al., 2015; PDB ID: 5FLX, individual panels represent different orientations (rotated by 90°).

7 Jan

New colleague in the lab: Andreas Horn

AndreasThe new year has just started and already there are some great news: Andreas Horn joined the lab as a PhD student! His PhD project will focus on a novel strategy that we have recently developed which allows to map protein-RNA interaction with high resolution in a parallel fashion. Welcome to the lab!

17 Dec

Season’s Greetings

Lab-Christmas-2015With christmas time approaching, we would like to thank our colleagues and collaborators for a wonderful and productive year! Also we would like to specifically thank the funding agencies for their very generous support that helps us to pursue our scientific goals!

Merry Christmas, a relaxing holiday season and a happy and successful New Year!

16 Dec

Fellowship for Stefan Reich

JHS_Logo_RGBWe are very happy to announce that Stefan Reich was awarded a fellowship from the Joachim Herz Stiftung!

‘I am very happy that my application for an Add-on Fellowship for Interdisciplinary Science from the Joachim Herz Stiftung was successful. This now gives me the opportunity to attend conferences and additional courses in bioinformatics which will support our work. Personally, I hope to gain further insight into data analysis which will pave the way to success in my doctoral thesis. For this reason I want to thank the Joachim Herz Stiftung very much for the generous support and I am looking forward to the first meeting with the other fellows in March 2016.’

-Stefan Reich, PhD student

1 Aug

Great news: Second funding period for Collaborative Research Centre 960 granted

SFB Mitglieder kleinThe Collaborative Research Centre 960 (SFB960) – Ribosome formation: principles of RNP biogenesis and control of their function has been extended for another funding period! We are now part of the SFB960 and we are very grateful for the financial support by the Deutsche Forschungsgemeinschaft (DFG) that allows us to address exciting scientific questions (see project B11).

Pictured above: the principal investigators of the SFB 960

17 Jun

E:med webpage online

The E:med webpage has just become live! E:med aims to combine life-sciences and informatics to create systems-wide approaches to address important questions in disease. We are very grateful that our SUPR-G junior consortium was selected to become part of this great initiative!

Logo_eMed_cmyk

 

3 Jun

New coworker: Stefan Reich

Stefan2We have a new colleague in the lab! We are very happy to announce that beginning of the month Stefan Reich has joined the lab as a PhD student! Stefan will work on deciphering the cellular reprogramming of translation during the unfolded protein response. Within the BMBF-funded SUPR-G network (Systems Biology of the Unfolded Protein Responsse in Glioma) he will collaborate with the groups of Christiane Knobbe-Thomsen (Heinrich Heine University Düsseldorf), Robert Ahrends (Leibniz Institute for Analytical Biosciences, ISAS, Dortmund), Grischa Tödt (European Molecular Biology Laboratory, EMBL, Heidelberg), and Björn Tews (German Cancer Research Center, DKFZ, Heidelberg). Welcome to Regensburg and welcome to the lab!

26 Mar

Labtours in the Biochemistry Department

Nacht-schafft-wissenThe initiative ‚Nacht schafft Wissen‘ by the city of Regensburg provides an opportunity to gain insight into the research and work that is conducted within numerous companies, the technical university of applied sciences, the university of Regensburg and its hospital. For this a number of talks and tours are offered to interested visitors. Rebecca Moschall from the lab will actively participate by guiding lab visits in the biochemistry department and explaining about the research that is conducted. We are very much looking forward to welcoming you on April 24th!

 (picture with permission from city of Regensburg)