Part B

The overarching goal of Part B is to enlarge the current understanding of the functional role of RNAs and RNA-protein complexes in biological processes and to unravel important aspects of RNA-based regulation.

The role of miRNAs in cardiovascular functions is investigated and the description of interactions will be supported by research on light-regulatable miRNAs and antagomirs in human cell lines. Furthermore, the impact of miRNAs on the example of miRNA-181 on the regulation of localized translation in neurons is studied. Here, the chemical and biological expertise is unified to establish light based antimiR-RNA to study the spatial function of miRNAs.

The gRNA and gRNA/pre-mRNA interactions as well as the dynamics within the editosome are investigated. Also, further optimization of SHAPE for structure probing of RNAs together will contribute to the understanding of fundamental processes concerning RNA homeostasis and its post-transcriptional processing and might lead to the identification of a potential drug.

New insights into this new regulatory mechanism are to be given by the structural analysis of such RNA-polymerase-ribosome complexes on a nascent chain in vitro, in situ and in vivo by cryo-electron tomography. It is our aim to provide structural information about functional interactions in the bacterial gene expression machinery in situ and we will shed light on the regulation of this essential machinery.

The investigation on the RNA – ATPase ABCE1 interactions should determine the binding sites and give descriptions for the structural changes. This study will yield a molecular and structural understanding of ribosome recycling during translation and will unravel the function of ABCE1 in ribosome biogenesis. The latter process involves many factors such as small nuclear RNAs (snoRNA) and proteins interacting with either the snoRNAs and/or the pre-rRNA to catalyse the formation of the two subunits of the ribosomes.

The analysis of components involved in plant ribosome biogenesis is started. Since it is known that a basic set of ribosome assembly factors is also conserved in plants, the function of these conserved RNA binding ribosome biogenesis factors will also be studied at the functional and the structural level. The long-term goal is therefore to describe the mechanistic and structural properties of plant specific adaptations to the ribosome biogenesis pathway.

This research is complemented by the investigation of the RNA-guided interactions of Nep1 on the one hand and at the D-cleavage site on the other hand. These RNA-protein interactions central to the ribosome biogenesis are investigated at the molecular level by biophysical and structural techniques.

Single-Molecule FRET was established in order to investigate global conformational changes on time scales and unter experimental conditions not accessible to NMR or EPR. Therefore, FRET will be applied to full-length riboswitches already investigated within the CRC and to the Box-H/ACA-RNA containing snoRNPs paralleling the EPR-experiments on a similar complex.

The functional dependence of SR proteins on the interacting RNA-elements will be investigated by a Comprehensive Functional Analysis of SR Proteins. Moreover, the impact of RNA-element based RNP formation on functional diversification is studied. It is expected that contributions will be made to the refinement of the model integrating splicing into the complex network of mRNA biogenesis.

The global identification of regulatory RNA elements for splicing will be deepened to describe the structure-function relationships of such elements, which is envisioned to be the prerequisite for Splicing Factor Assembly and Splicing Efficiency.