RNA turnover in plant stress responses

• Applicants: Professor Dr. Sascha Laubinger; Professor Dr. Christian Schmitz-Linneweber
• Subject Area: Plant Physiology
• Term: since 2020
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 433113158

Modulating the stability of RNAs is a key feature of gene expression regulation. While housekeeping genes usually produce highly stable RNAs, stress-responsive genes often encode RNAs with low stability. This allows rapid RNA turnover; a feature particularly important for plants, which have to adapt quickly to changing environmental conditions and stresses. The pathways that execute RNA degradation in plants are well understood. However, it is largely unknown how stresses destabilize specific RNAs, and how target specificity of RNA degrading enzymes is controlled.To address these questions, we will apply our recently developed ERIC-sequencing technology to stressed and unstressed Arabidopsis thaliana plants. Traditionally, RNA decay over time and RNA half-lives have been determined after harsh treatments with highly toxic transcriptional inhibitors such as actinomycin D and cordycepin. We developed a novel method (ERIC-seq), which employs metabolic RNA labeling using the non-toxic 5-ethynyl uridine (5-EU) combined with RNA sequencing. This allowed us for the first time to determine RNA stability non-invasively in plants. We will apply this technique to study the stability of nuclear and chloroplast-encoded RNAs under a diverse set of abiotic stress conditions. In addition, we will study the role of specific cytosolic and plastidic RNA degradation and stabilization pathways under selected stress conditions. This approach enables us to identify stress-specific RNA sequence features, that (1) ensure RNA stabilization and destabilization under abiotic stress conditions, and that (2) determine the specificity of RNA degradation pathways for subpopulations of RNAs. Such sequence elements will be functionally studied, linked to specific endonucleases, and used to identify novel trans-regulatory RNA stability factors. As a major deliverable, our approach will identify the impact of RNA turn-over on gene regulation during stress on a transcriptome-wide scale.

• DFG Programme: Research Grants