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Projects / Principal Investigator

Prof. Dr. Albrecht Bindereif, Justus-Liebig-Universität Gießen

Circular RNA networks in the human system: biogenesis, RNA-protein interactions, and translation potential

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Specific aims of this project are, first, to identify and investigate factors involved in circular RNA biogenesis (circRNA processing and circRNA export); second, to characterize RNA-protein complex (circRNP) formation; and third, to systematically elucidate the potential of circRNAs to be translated into protein. In general, our project will search for networks linking circRNA biogenesis, protein binding, and translation potential.

Prof. Dr. Katja Sträßer, Justus-Liebig-Universität Gießen

Function of Tho1/CIP29 in nuclear mRNP formation

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mRNA is synthesized by RNA polymerase II in the nucleus of eukaryotic cells. Already co-transcriptionally, the mRNA is processed (capped and spliced) as well as packaged into a ribonucleoprotein particle (mRNP) by nuclear RNA-binding proteins. The latter is important for mRNA stability, nuclear mRNA export and even cytoplasmic processes such as translation. Thus, nuclear mRNP formation is an important step to control gene expression. A protein called Tho1/CIP29 is known to be important for nuclear mRNP formation. However, the molecular function of Tho1/CIP29 and its regulation has remained elusive. Thus, in this project, the function of Tho1/CIP29 in nuclear mRNP formation shall be elucidated. Specifically, we aim to unravel, how Tho1/CIP29 is recruited to the mRNA, how Tho1/CIP29 takes part in nuclear mRNP formation and how Tho1 is regulated or regulates other proteins involved in mRNP formation. Taken together, the results of this project are expected to bring novel insights in nuclear mRNP formation, a process essential for correct gene expression.

Prof. Dr. Peter Friedhoff, Justus-Liebig-Universität Gießen

Function of the RNA helicase Sub2 from Saccharomyces cerevisiae: mechanistic FRET- and crosslinking-based studies

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Specific aims of this project are, first, to determine how Sub2's activities (ATPase, RNA binding, helicase) are regulated by its interaction partners, the THO complex, Yra1, and Tho1 (see project Strä&szliger;) in vitro and, second, to dissect the molecular functions of Sub2 in nuclear mRNP biogenesis and export in vivo. To do so, protein variants selectively impaired in either substrate interaction (ATP/RNA binding) or in protein-protein interactions will be used. Taken together, our project will unravel at the molecular level the function of Sub2 in nuclear mRNP formation and export.

Dr. Oliver Rossbach, Justus-Liebig-Universität Gießen

Artificial Circular RNA Sponges as a Novel Therapeutic Tool in Molecular Biology and Medicine

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Circular RNAs (circRNAs) have recently become a focus of biomedical research. A cellular circRNA, CDR1as/ciRS-7, was identified as a neuronal miRNA sponge that sequesters and functionally inhibits miRNA-7 and regulates its homeostasis. Due to their elevated stability compared to linear RNAs, circRNAs represent a promising tool in biotechnological applications. We have developed artificial circular RNAs produced in a cell-free system as molecular tools to inhibit cellular miRNAs function when transfected into cells. This was demonstrated in a proof-of-principle study where Hepatitis C Virus propagation was halted by sequestering miRNA-122.

In the first funding period, we have optimized and streamlined the circRNA production process, and developed a circRNA decoy which targets the oncogenic miRNA-21 and thereby inhibits tumor growth in both 2D and 3D cell culture, as well as in Xenograft mice when systemically delivered. Throughout these studies, the question arose if the cellular RNA sensors of the innate immunity responsible for viral RNA recognition, will also trigger an immune response to artificial circRNAs. Foreign RNAs are recognized by sensors as PKR, TLRs, RIG-I and MDA by distinctive features on the RNA. Our current results suggest that the cell cannot recognize foreign RNA if it is delivered as a covalently closed circle.

Prof. Dr. Gabriele Klug, Justus-Liebig-Universität Gießen

Mechanisms of maturation and interplay of bacterial sRNAs and mRNAs, which are co-transcribed

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Specific aims of the project are first, to determine the factors involved in maturation and processing of sRNAs in R. sphaeroides; second, to test, how stress conditions affect maturation and processing; and third, to answer the question, whether co-transcription of protein- and sRNA-coding genes is important for biological function.

Prof. Dr. Elena Evguenieva-Hackenberg, Justus-Liebig-Universität Gießen

Posttranscriptional regulation of S-adenosylmethionine and N6-methyladenosine modification of RNA in the alpha-proteobacterium Sinorhizobium meliloti

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Specific aims of this project are, first, to uncover the post-transcriptional mechanisms leading to increased SAM concentration upon depletion of either RNase E or RNase J in S. meliloti; and second, to identify ″hot spots″ of m6A methylation in mRNAs and regulatory RNAs in this organism as a first step towards the identification of the corresponding methylating enzyme and our understanding of the physiological role of this RNA modification in bacteria. Altogether, we aim to reveal new mechanisms for post-transcriptional regulation of gene expression in bacteria.

Prof. Dr. Alexander Goesmann, Justus-Liebig-Universität Gießen

Scalable bioinformatics workflows for automated RNA-based sequence data processing: Implementation of bioinformatics workflows as scale-out solutions in Cloud computing environments

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Specific aims of this project are, first, to identify and investigate analysis tools containing processing steps within RNA data analysis workflows that are well suited for parallelization in a Cloud computing environment; second, to choose the optimal software framework (e.g. Hadoop, Spark) for a most efficient parallelization and to implement the individual processing steps in a scalable way; and third, to systematically integrate the newly implemented analysis modules into larger data processing pipelines based on Galaxy, Conveyor, Nextflow (, or Snakemake. In general, our project aims at supporting our collaborating partners within this training group by implementing fully automated analysis workflows that are easy to use and that can be scaled-out efficiently in Cloud computing environments. We will also extend our Compuverde vNAS storage system that is attached to our Cloud infrastructure to provide sufficient space for data storage for the members of the GRK. Finally, we will integrate all workflows into our ReadXplorer software and make them easily accessible for various groups of users with individual-use case scenarios.

Dr. Aline Koch and Prof. Dr. Karl-Heinz Kogel, Justus-Liebig-Universität Gießen

Towards an RNAi-based control of plant diseases: Research into its mechanistic basis

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Given the current state of knowledge, the overall scientific goal of this project is to elucidate the molecular mechanism(s) of RNAi-based plant protection in a fungal pathosystem. The specific aims are: first, to identify and further characterize plant and fungal RNAi-associated factors that are involved in HIGS and SIGS, respectively, by assessing a set of Arabidopsis RNAi mutants; second, to characterize plant ARGONAUTE (AGO) proteins involved in HIGS and SIGS by assessing siRNA-AGO protein complex formation; and third, to explore the hypothesis that RNA signals (dsRNA/siRNA) are translocated from the plant to the fungus via exosomes.

Prof. Dr. Michael Niepmann, Justus-Liebig-Universität Gießen

Controlling the switch from viral RNA genome translation to genome replication: the moonlighting function of cellular Glycyl-tRNA synthetase during picornavirus infection

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Early in the life cycle of a picornavirus, the incoming viral plus strand RNA genome must first be translated by cellular ribosomes, followed by a switch to minus strand synthesis by the viral replicase starting from the 3´-end. Such RNA viruses often employ cellular proteins which act on the viral RNA in non-canonical ("moonlighting") functions for regulatory purposes. Glycyl-tRNA synthetase (GARS) binds to the 5´UTR of Poliovirus and stimulates viral translation. In contrast, the RNA genome of the related Mengovirus recruits the GARS protein to a conserved RNA element downstream of the polyprotein termination codon. We hypothesize that GARS is a key factor for regulating a switch from Mengovirus RNA translation to genome replication. In the current project, we aim at characterizing GARS function in viral gene expression and to identify cellular mRNAs that are bound and possibly regulated by GARS.

Prof. Dr. Roland K. Hartmann, Philipps-Universität Marburg

Regulation of transcription by 6S RNAs in Bacteria

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Specific aims of this project are, first, to characterize the regulatory function of 6S-1 RNA through analyzing the phenotypic as well as transcriptomic and proteomic consequences of 6S RNA deletions in a real wild-type strain, B. subtilis NCIB 3610; second, to mechanistically understand the pRNA-induced release of 6S-1 RNA from complexes with RNA polymerase, using single-molecule total internal reflection fluorescence microscopy (TIRF); third, in vitro iCLIP analyses to identify 6S-1 RNA nucleotides in contact with σA-RNAP; fourth, to unveil processing and decay of the two regulatory 6S RNAs in B. subtilis.

Prof. Dr. Thomas Böttger, Max-Planck-Institut für Herz- und Lungenforschung, Bad Nauheim

Molecular analysis of in vivo functions of lincRNA in contractile tissues

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Specific aims of this project are, first, to identify physiological functions of lncRNAs in muscle or brown adipose tissue; second, to understand the molecular interactions of lncRNAs mediating the function of these lncRNAs, and third, to develop unifying concepts of lncRNA function with special emphasis on mechanisms of transcriptional regulation and epigenetics in development, physiology and regeneration of muscle tissue.

Dr. Andre Schneider, Max-Planck-Institut für Herz- und Lungenforschung, Bad Nauheim

The impact of RNA-binding proteins and alternative splicing in cardiovascular diseases

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Specific aims of this project are, first, to investigate the impact of the RBP families Rbpms/Rbpms2 and Matr3/Rbm20 in linear and circular splicing processes within the cardiovascular system (myocardium and vascular smooth muscle); and second, to systematically elucidate causes and consequences of Rbpms subcellular localization shift under myocardial stress conditions.

Dr. Cornelia Kilchert (Guest PI), Emmy Noether Research Group Leader, Justus-Liebig-Universität Gießen

Nuclear RNA surveillance

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Many RNAs that are transcribed from the genome are rapidly degraded – others escape surveillance, are exported into the cytoplasm, and assume their function in the biosynthetic process. We want to understand the molecular signals that determine this choice. In particular, we investigate how RNA fate decisions are molecularly encoded in the ribonucleoprotein (RNP) coat of the RNA, which communicates the status of the RNA to the surrounding environment. Within the RTG, Philip and Ebru study proteins that promote RNA degradation by the exosome complex, and ribonucleoprotein (RNP) remodelling helicases that “update” the composition of the RNP coat as RNA processing progresses.Specific aims of this project are, first, to identify and investigate factors involved in circular RNA biogenesis (circRNA processing and circRNA export); second, to characterize RNA-protein complex (circRNP) formation; and third, to systematically elucidate the potential of circRNAs to be translated into protein. In general, our project will search for networks linking circRNA biogenesis, protein binding, and translation potential.