Group Waldsich

Exploring RNA folding: from structure to function

RNAs regulate biology: In the past years it has become increasingly evident that RNA is the driving force in most cellular processes. Although these RNAs are highly diverse and fulfill very different tasks, they share their strict dependence on acquiring a specific 3D architecture to be functional. The process of folding describes how RNA undergoes the transition from a disordered, unfolded state to the native, functional conformation. Our research focuses on understanding this most essential aspect of RNA function by investigating RNA structure and folding pathways. Specifically, we aim to provide novel insights into protein-facilitated RNA folding and how RNAs fold in the living cell. Little is known about how RNA folds in vivo and how they interact with their targets despite RNA’s importance for cell viability. Therefore, it is of fundamental importance to gain insights into the forces driving RNA folding in vivo and to establish the contribution and impact of the cellular environment, in order to understand the basic mechanism of these RNA-dependent processes. Catalytic RNAs, in particular group II introns, are the best-suited model system to study RNA folding in the living cell, as their structure and folding pathways are well characterized in vitro and formation of the native conformation can be measured as a function of catalysis. Therefore, we investigate the intracellular folding pathway of the Sc. ai5g group II intron. Importantly, Sc. ai5g and other yeast mitochondrial introns depend on trans-acting protein factors for efficient splicing in vivo.

Consequently, we are interested in exploring how these proteins shape folding of its target RNAs. This allows us to derive principles governing in vivo RNA folding facilitated by proteins and other cellular factors. Aside from studying catalytic RNA, we are fascinated by Telomerase; an RNP that has received considerable attention because of its significant up-regulation in the majority of cancer cells and its role in preventing chromosomal instability and senescence as well as in inherited human disorders. In spite of the high level of interest in the bio-medical importance of telomerase, telomerase RNA and protein components have largely eluded structural characterization. In this regard, we are interested in exploring the structure of telomerase RNA and in studying the interplay of RNA folding and RNP assembly. Ultimately, deciphering the rules governing RNA folding will advance our understanding of the basic mechanism of RNA-dependent processes, like self-splicing and telomere addition, and the role of RNA in disease.

RNA folding in the living cell: Group II introns and their intracellular structure

Despite RNA¡'s importance for cell viability little is known about how RNA folds in vivo and how they interact with their targets. Therefore, it is of fundamental importance to gain insights into the forces driving RNA folding in vivo and to establish the contribution and impact of the cellular environment, in order to understand the basic mechanism of these RNA-dependent processes. Catalytic RNAs, in particular group II introns, are the best-suited model system to study RNA folding in the living cell, as their structure and folding pathways are well characterized in vitro and formation of the native conformation can be measured as a function of catalysis. Therefore, we investigate the intracellular folding pathway of the Sc. ai5γ group II intron. Importantly, Sc. ai5γ and other yeast mitochondrial introns depend on trans-acting protein factors for efficient splicing in vivo. Consequently, we are interested in exploring how these proteins shape folding of its target RNAs. This allows us to derive principles governing in vivo RNA folding facilitated by proteins and other cellular factors.

Telomerase: RNA-protein interactions and RNP assembly

Telomerase is a large ribonucleoprotein complex that plays a major role in the maintenance of telomeres, which form a protective cap of chromosome ends. Telomerases from all species contain an essential RNA component (TER), a unique reverse transcriptase protein (TERT) and several accessory proteins involved in assembly, accumulation and localization. TERT uses the intrinsic RNA as template for the extension of the telomere, whereby shortening of telomeres below a critical length leads to cell aging. Telomerase has received considerable attention because of its significant up-regulation in the majority (>90%) of cancer cells and its role in preventing chromosomal instability and senescence. In addition, mutations in both TER and the telomerase accessory protein dyskerin have been linked to the inherited human disorders, Dyskeratosis Congenita and Aplastic Anemia. In spite of the high level of interest in the biological and medical importance of telomerase, telomerase RNA and protein components have largely eluded structural characterization. In this regard, we are interested in exploring the structure of telomerase RNA and in studying the interplay of RNA folding and RNP assembly.

Publications

Wildauer, Michael; Zemora, Georgeta; Liebeg, Andreas; Heisig, Verena; Waldsich, Christina (2014). Chemical probing of RNA in living cells. Meth Mol Biol;1086:159-76. PMID: 24136603

Sachsenmaier, Nora; Handl, Stefan; Debeljak, Franka; Waldsich, Christina (2014). Mapping RNA structure in vitro using nucleobase-specific probes. Meth Mol Biol;1086:79-94. PMID: 24136599

Flores, Samuel Coulbourn; Zemora, Georgeta; Waldsich, Christina (2013). Insights into diseases of human telomerase from dynamical modeling. Pacific Symposium on Biocomputing.:200-11. PMID: 23424125

Cruz, José Almeida; Blanchet, Marc-Frédérick; Boniecki, Michal; Bujnicki, Janusz M; Chen, Shi-Jie; Cao, Song; Das, Rhiju; Ding, Feng; Dokholyan, Nikolay V; Flores, Samuel Coulbourn; Huang, Lili; Lavender, Christopher A; Lisi, Véronique; Major, François; Mikolajczak, Katarzyna; Patel, Dinshaw J; Philips, Anna; Puton, Tomasz; Santalucia, John; Sijenyi, Fredrick; Hermann, Thomas; Rother, Kristian; Rother, Magdalena; Serganov, Alexander; Skorupski, Marcin; Soltysinski, Tomasz; Sripakdeevong, Parin; Tuszynska, Irina; Weeks, Kevin M; Waldsich, Christina; Wildauer, Michael; Leontis, Neocles B; Westhof, Eric (2012). RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction. RNA;18(4):610-25. PMID: 22361291

Sachsenmaier, Nora; Waldsich, Christina (2012). Mss116p: A DEAD-box protein facilitates RNA folding. RNA BIOL;10(1):70-81. PMID: 23064153

Tian, Nan; Yang, Yun; Sachsenmaier, Nora; Muggenhumer, Dominik; Bi, Jingpei; Waldsich, Christina; Jantsch, Michael F; Jin, Yongfeng (2011). A structural determinant required for RNA editing. NUCLEIC ACIDS RES(39):5669-81. PMID: 21427087

Lorenz, C; Gesell, T; Zimmermann, B; Schoeberl, U; Bilusic, I; Rajkowitsch, L; Waldsich, C; von Haeseler, A; Schroeder, R (2010). Genomic SELEX for Hfq-binding RNAs identifies genomic aptamers predominantly in antisense transcripts. NUCLEIC ACIDS RES. PMID: 20348540

Liebeg, Andreas; Mayer, Oliver; Waldsich, Christina (2010). DEAD-box protein facilitated RNA folding in vivo. RNA BIOL. PMID: 21045551

Zemora, Georgeta; Waldsich, Christina (2010). RNA folding in living cells. RNA BIOL. PMID: 21045541

Liebeg, Andreas; Waldsich, Christina (2009). Probing RNA structure within living cells. METHOD ENZYMOL. PMID: 20946772

Waldsich, Christina; Pyle, Anna Marie (2008). A kinetic intermediate that regulates proper folding of a group II intron RNA. J MOL BIOL. PMID: 18022197

Waldsich, Christina (2008). Dissecting RNA folding by nucleotide analog interference mapping (NAIM). NAT PROTOC. PMID: 18451789

Waldsich, Christina; Pyle, Anna Marie (2007). A folding control element for tertiary collapse of a group II intron ribozyme. Nat Struct Mol Biol. PMID: 17143279

Pyle, Anna Marie; Fedorova, Olga; Waldsich, Christina (2007). Folding of group II introns: a model system for large, multidomain RNAs? TRENDS BIOCHEM SCI. PMID: 17289393

Fedorova, Olga; Waldsich, Christina; Pyle, Anna Marie (2007). Group II intron folding under near-physiological conditions: collapsing to the near-native state. J MOL BIOL. PMID: 17196976

Rajkowitsch, Lukas; Chen, Doris; Stampfl, Sabine; Semrad, Katharina; Waldsich, Christina; Mayer, Oliver; Jantsch, Michael F; Konrat, Robert; Bläsi, Udo; Schroeder, Renée (2007). RNA chaperones, RNA annealers and RNA helicases. RNA BIOL. PMID: 18347437