Projects & People

Functional characterization of the antagonistic interactors Sub2 and Tho1 in nuclear mRNP biogenesis

Molecular mechanism of Sub2 and Tho1 in nuclear mRNP biogenesis and RNA:DNA hybrid prevention

Analysis of interactions of viral proteins with cellular RNAs - how RNA viruses alter RNA networks

The molecular interactions between viral proteins and components inside of host cell are an important and yet understudied field in RNA virology. The aim of our project is to systematically analyze the influence of RNA virus infection on the cellular mRNA life cycle across various virus families, and to identify interaction surfaces where therapeutic RNAs can interfere. We will first identify viral proteins that directly bind to RNAs and characterize their cellular RNA interaction partners using biochemical in vivo binding studies and sequencing (CLIP; UV-crosslinking and immunoprecipitation). Second, we will monitor changes in cellular mRNA processing and turnover induced by viral protein binding during infection, and third, we will develop and produce circRNA decoys that can interfere with these interactions, aimed at inhibiting crucial steps in the viral replication cycle. Research will focus on alpha- and beta-coronaviruses such as HCoV-229E and SARS-CoV-2 (positive-strand RNA viruses); and the Rift Valley Fever Virus (RVFV; a negative-strand Phlebovirus). Link AG Rossbach

Scalable, reproducible and FAIR bioinformatics workflows for automated analysis of multi-dimensional RNA-based viral sequence data

Standardized and automated data processing is a crucial prerequisite to achieve valid, comparable and reproducible results in all kinds of RNA-related experiments. To support this task, we develop tailored analysis workflows based on the needs of and in close cooperation with the partners in the RTG2355. Besides the analysis of RNA data, a further focus of our workflow development is the analysis, evaluation and visualization of multi-dimensional viral datasets. Newly developed bioinformatics workflows will be integrated into the open data management platform openBIS, furthermore a workflow repository will be created in close collaboration with the National Research Data Infrastructures (NFDIs) to ensure compliance with the standards developed in these consortia. Data management will be developed in compliance with the FAIR principles, i.e., experimental data and analysis results are findable, accessible, interoperable, and reusable. Link AG Goesmann

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

Picornaviruses evolved secondary structures in their genomic RNAs that bind proteins of the host cell and use them in so-called "moonlighting" functions to facilitate translation of their own genome. A tRNA anticodon stem-loop-like structure in the 3´UTR of Mengovirus genomic RNA specifically binds to the cellular enzyme Glycyl-tRNA synthetase (GARS). Translation of the Mengovirus full length genome in cells is impaired by mutation of this GARS binding element (GBE) directly after transfection, independent of the activity of the viral polymerase. Also, translation of short artificial reporter RNAs containing the Mengovirus untranslated regions is impaired by mutation of the GBE. Thus, the GBE is involved in Mengovirus translation regulation. We aim to further characterize the interaction of this GARS binding element with the cellular translation machinery and its impact on the viral replication cycle. Link AG Niepmann

Viral and cellular regulators of the mRNA translation inhibitor PKR

Structural and functional characterization of two putative cis-acting RNA elements in the 3'-untranslated regions of coronavirus genomes

Replication and transcription of coronavirus genomes are mediated by the so-called replication-transcription complex (RTC) comprised of more than a dozen proteins. However, several specific cis-acting RNA structural and sequence elements located in the terminal regions of the viral genomic RNA are also thought to be involved. Some of these RNA elements were suggested to be conserved among alpha- and beta-coronaviruses, indicating important roles in viral replication. We study the biological functions of two of these conserved RNA elements and their interactions with components of the RTC and with host cell proteins using a combination of coronavirus reverse genetics, proteomics, and RNA biochemistry approaches (e.g., RNA structure probing, RNA-protein interactions using RNA-Map and reporter gene assays). Link AG Ziebuhr

Regulation of bacterial transcription by 6S RNAs

Non-coding 6S RNAs regulate transcription by binding to the active site of specific bacterial RNA polymerase (RNAP) holoenzymes. RNAP can reverse this inhibition by utilizing 6S RNA as a template for the synthesis of short transcripts that remain bound to 6S RNA and rearrange its structure, leading to dissociation of 6S RNA from RNAP. Bacillus subtilis expresses two 6S RNA paralogs whose gene knockouts lead to very different and rather specific phenotypes in a wild-type strain (NCIB 3610): The ∆6S-1 RNA strain grows to lower optical density during extended stationary phase, while the ∆6S-2 RNA strain shows derepressed biofilm formation, retarded swarming activity and accelerated spore formation. The ∆6S-1&2 double deletion strain displays prolonged lag phases of growth under oxidative, high salt and alkaline stress conditions, in addition to decelerated spore formation. We aim to understand the causes of these phenotypes on the molecular and moleculargenetic level by applying biochemical, genetic and global analysis (transcriptomics, proteomics, ChIP-seq) methodologies. Link AG Hartmann

Epitranscriptomic analysis of the RNA stability in Escherichia coli during T4 phage infection

Since dynamic regulation of RNA stability during T4 phage infection of E. coli has been identified for both host and phage transcripts, our project aims to determine and characterize the molecular mechanisms that regulate RNA stability during the infection process. For this purpose, we will first investigate the functional role of nucleases and RNA-binding proteins on RNA stability and processing during phage infection. Second, we will apply our NAD captureSeq approach to analyze the presence and function of E. coli and T4 NAD-capped RNA during infection, and third, we will focus on the interaction of RNA-binding proteins with small regulatory RNAs (sRNAs) present in E. coli and in T4 phages by performing cross-linking (iCLIP) experiments. This study will broaden our understanding of how T4 and E. coli nucleases and RNA binding proteins orchestrate RNA stability during infection and how RNA modifications modulate RNA stability to trigger an effective T4 infection. Moreover, these biological insights may provide new knowledge for applications in biotechnology and medicine. Link AG Höfer

Molecular analysis of in vivo functions of lncRNAs in mammalian contractile tissues

We are specifically interested in a long non-coding RNA (lncRNA) that regulates differential splicing of a messenger RNA in striated muscle; malfunction of this lncRNA appears to be connected to cardiac hypertrophy. The aims of this project are therefore to identify, first, elements of the lncRNA that are essential for the regulation of alternative splicing, and second, proteins that might interact with the lncRNA and control its function. Third, we are interested in the consequences of the alternative splicing on the molecular as well as the physiological level. Link AG Böttger

Role of alternative splicing and circRNA function in adipogenesis, glucose homeostasis, and obesity

Post-transcriptional regulation of gene expression encompasses multiple processes including splicing, modification, editing, translation, transport, storage and turnover of RNAs. Our overall goal is to decipher the functional role of RNA binding proteins in regulating alternative splicing of linear mRNAs and circRNAs in adipogenesis, obesity as well as in cardiovascular diseases. Furthermore, we are investigating m6A modifications in the context of disease processes of the myocardium. Combining transgenic as well as viral-mediated gain- and loss-of-function approaches in vivo with cell culture systems, we are aiming to decipher and manipulate novel disease-relevant molecular pathways. Link AG Schneider

Deconstructing context-dependent regulatory miRNA networks in T cell development

Human health depends on the continuous generation of fresh immune cells, and a thorough understanding of the underlying molecular and cellular mechanisms is of great importance for improving treatment of many diseases. In this context, our laboratory investigates how post-transcriptional gene regulation and, more specifically, certain microRNAs (miRNAs) contribute to the formation of a functional yet non-autoreactive pool of peripheral T cells. miRNAs are key mediators of post-transcriptional gene regulation, serving as guides inducing degradation or translational inhibition of target mRNAs, and we aim to unravel how structural features of the mRNA targets, target site occupancy by RNA-binding proteins as well as competition and/or cooperativity between miRNAs contribute to miRNA function. Link AG Krueger

Algorithmic design of RNA secondary structure prediction tools

RNA is not a linear molecule, but folds onto itself by forming base pairs between nucleotides of the same strand, often establishing long-range interactions within the respective molecule. This so-called secondary structure significantly contributes to gene regulation, e.g., by changing accessibility of ribosome binding sites, other protein or RNA binding sites. We will make use of the experimentally derived structure probing data generated by various RTG groups to improve RNA secondary structure prediction tools, generating algorithms that suggest several possible secondary structures instead of only a single structural model. Link AG Janssen

Affiliated Postdocs