The plant splicing code: regulatory components and functions in developmental processes
Final Report Abstract
Eukaryotic mRNAs undergo complex processing during their lifetime, starting at the precursor mRNA stage with capping, alternative splicing (AS), and 3’ end processing and ending with mRNA decay in different compartments and via alternative routes. Many aspects of mRNA processing have been shown to be tightly regulated, thereby resulting in alternative outputs both on a qualitative and quantitative level. These observations have critical implications in the regulation of gene expression and for numerous aspects of eukaryotic development. The research in the Wachter group aims at providing novel insight into the regulation and functions of AS and RNA decay in plant development and stress responses. During funding in the Heisenberg program, three major lines of research have been pursued: 1) Characterizing AS control in seedling photomorphogenesis and flower development; 2) Deciphering novel components of the plant splicing code; 3) Investigating abiotic stress control of the RNA surveillance mechanism nonsense-mediated decay (NMD). In the course of this work, we were able to identify novel components linking AS and developmental processes in plants. Furthermore, we have established TRIBE, a method to identify in vivo interactions between RNA-binding proteins and their target RNAs, for the first time in plants. This tool will enable us to identify novel components and molecular mechanisms of AS control in plants. Using in vitro RNA-protein interaction methods and splicing reporter assays, we provided evidence that the effect of the splicing regulator Polypyrimidine Tract Binding Protein (PTB) on cassette exon inclusion or skipping can depend on the binding position relative to the regulated exon. Following up on the identification of the RSZ subfamily of Serine/Arginine-rich proteins as potential antagonists of PTBs, we have generated and characterized a set of rsz mis-expression lines for future studies of this possible splicing regulator interplay. Finally, we have demonstrated that several types of abiotic stresses including salt exposure lead to rapid NMD inhibition and NMD target stabilization. Understanding the molecular basis of NMD regulation under abiotic stress and examining possible functions of NMD target stabilization in the stress response are major goals of our current research in this project area. Taken together, our work has provided novel insight into the regulation and functions of AS and stressmodulated mRNA decay in plants. These findings further support the view that RNA-based mechanisms play key roles in diverse aspects of eukaryotic development. Our observations are not only of relevance to explore basic aspects in plant and RNA biology, but can also help to develop novel approaches in applied plant sciences such as engineering plants for enhanced resilience.
Publications
- (2016). Alternative Splicing Substantially Diversifies the Transcriptome during Early Photomorphogenesis and Correlates with the Energy Availability in Arabidopsis. Plant Cell 28: 2715-2734
Hartmann L, Drewe-Boss P, Wiessner T, Wagner G, Geue S, Lee HC, Obermüller DM, Kahles A, Behr J, Sinz FH, Rätsch G, Wachter A
(See online at https://doi.org/10.1105/tpc.16.00508) - (2018). Subcellular Compartmentation of Alternatively Spliced Transcripts Defines SERINE/ARGININE-RICH PROTEIN30 Expression. Plant Physiol 176: 2886-2903
Hartmann L, Wiessner T, Wachter A
(See online at https://doi.org/10.1104/pp.17.01260) - (2019) NMD-based gene regulation - a strategy for fitness enhancement in plants? Plant Cell Physiol
Ohtani M, Wachter A
(See online at https://doi.org/10.1093/pcp/pcz090) - (2019). Multifactorial and Species-Specific Feedback Regulation of the RNA Surveillance Pathway Nonsense-Mediated Decay in Plants. Plant Cell Physiol
Kesarwani AK, Lee CH, Ricca PR, Sullivan G, Faiss N, Wagner G, Wunderling A, Wachter A
(See online at https://doi.org/10.1093/pcp/pcz141)
