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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

Functional sequestration of hijacked cellular RNA-binding proteins from viral RNAs by circular RNA sponges

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This project is focused on the production and optimization of artificial circular RNA (circRNA) sponges that are used as tools in molecular medicine and biology. Recently we had demonstrated an efficient inhibition of Hepatitis C Virus (HCV) in cell culture system by engineered circRNAs that sequester the essential host factor microRNA-122. Now, we aim to extend the repertoire of artificial circRNA sponges and sequester other microRNAs and/or RNA-binding proteins that are relevant in human disease; at first, in HCV, since the virus hijacks many cellular proteins for its propagation.

The primary goal of the project is to determine the optimal high-affinity binding sites of specific host factors that positively affect HCV translation, as well as the binding site of the viral protease/helicase NS3. Secondly, we would construct and synthesize/express circular RNA sponges containing these binding sites and probe their sequestration efficiency in HCV reporter systems, including full-length infectious HCV. Thirdly, via monitoring the effects of these circRNA sponges on cellular RNAs, we investigate possible alterations in alternative splicing, mRNA export and/or translation. Ultimately, we aim to elucidate whether these circRNAs can be used to modulate aberrant mRNA processing events in the context of human disease. In collaborations with other groups, we explore if circular RNAs can also be applied to other viral and bacterial infections, cancer, as well as cardiovascular- and pulmonary disease.

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

tRNA mimicry: RNA signals in viral and cellular mRNAs that are regulated by glycyl-tRNA synthetase

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RNA viruses often recruit cellular RNA binding proteins to facilitate replication of their RNA genomes in the host cell. The cellular glycyl-tRNA synthetase (GARS) binds to a conserved tRNA-like element in Poliovirus RNA and regulates Poliovirus translation. Such GARS binding elements are also present in the genomic RNAs of other pathogenic Picornaviruses like Entero- and Coxsackieviruses. We want to characterize the role of GARS binding elements in Enterovirus gene expression, replication and pathogenesis. We will also search for possible GARS target sites in human mRNAs by global analyses of GARS binding to RNA.

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.

PD 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.