The research in our group aims at a better understanding of RNA-based mechanisms underlying plant developmental processes and stress responses. Our major focus is on the regulation of alternative precursor mRNA splicing (AS) and the RNA surveillance pathway nonsense-mediated decay (NMD). Our studies can be divided into four major topics:
1. The role of light- and sugar-regulated AS in seedling photomorphogenesis
2. Identifying novel components of the plant splicing code
3. The role of structured mRNA elements in gene regulation
4. Regulation and functions of NMD in plant stress responses & development
The following sections will provide a short overview of these four major lines of research. Furthermore, references to selected publications from our group will be provided for further reading.
1. The role of light- and sugar-regulated AS in seedling photomorphogenesis
Research from our group and other researchers has revealed the major impact of AS in response to changing light conditions, including the fundamental developmental switch of etiolated seedlings from skoto- to photomorphogenesis. This work has demonstrated that light and sugar signals can trigger numerous AS changes and thereby control plant development. Major open questions in this research field refer to the mechanisms and signalling pathways underlying these alternative splicing programs.
Further reading: Hartmann et al. (2016 & 2018).
2. Identifying novel components of the plant splicing code
Most AS decisions are the outcome of an intricate interplay between cis-regulatory elements on the precursor mRNA and trans-acting factors, such as splicing regulatory proteins. Given the large number of RNA-binding proteins in higher eukaryotes and the low level of sequence conservation of RNA motifs, identifying the molecular components of the splicing code is a major challenge. Despite major advantages based on the characterisation of individual splicing regulators and methodological breakthroughs making use of next generation sequencing techniques, the regulatory mechanisms underlying the majority of AS events in plants remain unknown. In our research, we use established methods and develop novel techniques to provide novel insight into AS control in plants. Furthermore, using mutant characterisation and physiological studies we aim at gaining a better understanding of the functional relevance of regulated AS in plants.
Further reading: Rühl et al. (2012).
3. The role of structured mRNA elements in gene regulation
RNA is well-known to fold into complex structures that can fulfill fundamental functions in biology, such as transfer RNAs and ribosomal RNAs in the process of protein biosynthesis. While mRNAs represent the most diverse and largest class of RNAs in the cell, their folding potential and in particular the biological functions associated with it were discovered only quite recently. For example, so-called riboswitches are mRNA domains that can sense metabolites and other small molecules and transform this information into a gene-regulatory response. In filamentous fungi and plants, riboswitches sensing thiamin pyrophosphate were found to control expression of thiamin biosynthesis genes on the level of AS. In our current research, we study the functions of evolutionary conserved mRNA motifs associated with AS in plants.
Further reading: Wachter (2014).
4. Regulation and functions of NMD in plant stress responses & development
NMD is a eukaryotic RNA surveillance pathway triggering degradation of mRNAs upon translation termination in an unusual context, e.g. as a consequence of an unusually long 3’ untranslated region. Numerous aberrant and physiological mRNAs were found to be regulated via NMD, highlighting its dual function in quality control and gene regulation. Interestingly, NMD can be inhibited upon diverse stresses in animals and plants and can function as a positive regulator of the stress response via stabilization of mRNAs from stress-related genes. So far, the mechanism of NMD inhibition under stress is unknown in plants. Furthermore, for most types of stresses and in particular abiotic stress, the biological function of NMD inactivation has not been investigated. Addressing these central questions regarding NMD regulation and functions under stress is the major focus of our research in this project.
Further reading: Ohtani & Wachter (2019), Kesarwani et al. (2019).