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)

 

 

4 Aug

Sino-German Symposium on RNA Biology

Rauischholzhausen-symposium

Jan's webpage

The ‘Sino-German Symposium on RNA Biology and human disease: from Molecular Mechanisms to Global Networks‘ took place from July 25-27 at the beautiful castle ‘Schloss Rauischholzhausen’ in the middle of Hessia. Albrecht Bindereif (Justus-Liebig-University of Giessen, Germany) and Zefeng Wang (CAS-MPG Partner  Institute for Computational Biology, Shanghai, P.R. China) invited more than 30 participants from China and Germany to discuss the latest findings in RNA biology and to forge scientific sino-german collaborations. A great symposium and a great experience, meeting old and new colleagues from China and making new friends.

 

Many thanks to Jingyi Hui (IBCB Shanghai) for the translation into chinese! Picture courtsey of Silke Schreiner, University of Giessen

20 Jul

RNA 2016

RNA-Japan-LogoRNA 2016 – The 21st annual meeting of the RNA Society and the 18th annual meeting of the RNA Society of Japan took place in the lovely city of Kyoto from June 28th to July 2nd. It was a very exciting meeting in the former imperial capital of Japan. Brilliant keynote lectures and more than 20 sessions packed with exciting talks covered the entire field of RNA biology, providing the participants with a broad overview as well as exciting novel developments in RNA-based research. All this was complemented with tours to the cultural highlights of the surrounding city. A brilliant experience!

After this wonderful conference it is clear that I have to attend the next meeting of the RNA Society, too, which will take place in Prague from May 30th to June 3rd 2017. Looking forward to seeing you there!

Japan-Essen

 

 

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’.

30 May

August 2nd, 2016 – Guest speaker: Mandy Jeske, EMBL Heidelberg

Oskar localizationSave the date! On August second 5p.m. in H53, Mandy Jeske from the EMBL in Heidelberg will give a talk entitled: Exploring molecular mechanisms in the germ plasm.

Germ cells are an integral part of sexual reproduction. To segregate the germline from soma, during early development many animals assemble a specialized cytoplasm, which is called germ plasm. The molecular mechanisms that take place in and define the germ plasm are poorly understood.

In her talk Mandy Jeske from the EMBL in Heidelberg will discuss molecular functions of the Drosophila germ plasm nucleation protein Oskar. She will present the recently solved crystal structures of Oskar and discuss activities of previously uncharacterized protein domains. Furthermore, she will address the molecular functions of Vasa, a germ-line specific DEAD-box RNA helicase involved in the secondary piRNA pathway, and how a novel class of protein domains regulates Vasa’s enzymatic activity.

We are very much looking forward to Mandy’s visit, a fascinating talk and exciting discussions!

Oskar and Vasa

1 Apr

July 21st, 2016 – Guest speaker: Andrea Pauli, IMP Vienna

Andrea-PauliMark your calendar! On July 21st, Andrea Pauli from the Research Institute of Molecular Pathology (IMP), Vienna, Austria, will visit the University of Regensburg. Her major research interest is the function of short open reading frames in zebrafish development.

Recent findings have indicated that eukaryotic translation is far more complex than anticipated with the frequent translation of short open reading frames that were previously overlooked. This ‘pervasive translation’ includes regions that are predicted to encode short, conserved proteins, while other translated regions lack signatures of protein conservation and might serve gene-regulatory functions. This raises two important questions: what is the role of the translated regions in the regulation of gene expression, and what are the functions of the newly discovered short proteins/petides? In her talk entitled ‘Found in translation: from genomics to novel gene functions in zebrafish’ (2p.m. in H53), Andrea will share exciting insights into the functions and regulatory principles of these newly discovered short translated open reading frames (ORFs) employing zebrafish embryogenesis as a model system.

Andrea-Pauli-primer

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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°).

11 Mar

Nobel laureate Randy Schekman talks about unconventional secretion of protein and RNA

Photos courtsey of Andreas FuchsStudents of the Regensburg International Graduate School for Life Sciences (RIGeL) invited Randy Schekman (UC Berkeley) for an honorary lecture to Regensburg. In 2013, together with his colleagues James Rothmann (Yale University) and Thomas Südhof (Stanford University), Randy received the Nobel Prize for Medicine for his groundbreaking work on cellular trafficking. It was an exciting event with great science and lots of fun! (Photos courtsey of Andreas Fuchs)

7 Mar

Meeting of the DFG Research Unit 2333 ‘Macromolecular complexes in mRNA localization’ (FOR2333)

FOR2333LogoThe first meeting of the DFG Research Unit 2333 (FOR2333) took place on March 1st and 2nd in the beautiful town of Blaubeuren, famous for its resurgence the ‘Blautopf’ that feeds the Danube river.  FOR2333 receives funding from the DFG since beginning of 2016 to foster multidisciplinary research aiming to understand principles of gene regulation by directional mRNA transport and local translation. Unfortunately our application to become part of this exciting research team was not successful but nonetheless we were invited to participate in this wonderful meeting packed with talks about exciting research and novel findings. We are extremely happy for this opportunity and we are looking forward to continuing our collaborations with several groups of the consortium.

FOR Meeting(Photo courtsey of Dierk Niessing)