Transcriptional reprogramming in response to environmental cues: role of productive RNA polymerase II transcript elongation

• Applicant: Professor Dr. Klaus Grasser
• Subject Area: Plant Biochemistry and Biophysics ; Plant Genetics and Genomics ; Plant Cell and Developmental Biology
• Term: since 2026
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 584877090

The nuclear DNA of eukaryotic organisms is packaged into nucleosome particles. By restricting the accessibility of DNA nucleosomes repress the process of gene transcription. Accordingly, RNA polymerase II (RNAPII), the enzyme that transcribes protein-coding genes (synthesising mRNAs), requires different assistant factors, which facilitate productive transcript elongation on nucleosomal DNA templates. Among the proteins that promote the elongation phase of RNAPII transcription are the so-called transcript elongation factors (TEFs). They represent a heterogeneous group of proteins with diverse functions including modulating the catalytic properties of RNAPII or destabilising nucleosomes in the path of the enzyme, allowing efficient mRNA synthesis. In line with their function in gene transcription TEFs contribute to adjusting accurately cellular transcript levels. Thus, plant TEFs mediate vital developmental transitions including the switch from seed dormancy to germination and from vegetative to reproductive development. During the current funding period we have implemented investigations to study the involvement of TEFs in plant responses to environmental cues. Exploiting abiotic stress conditions (i.e. heat stress) that require transcriptional reprogramming, enabled us to gain insight into the functionality of different TEFs in plant responses to stressful conditions. Our findings indicate an intensive interplay of TEF function and nucleosomal properties along transcribed genes. Therefore, we intend to elaborate on this aspect during the coming funding period of this renewal proposal. We will use genome-wide differential micrococcus nuclease digestion assays that represent a powerful tool to examine nucleosome positioning/stability. This is combined with transcriptomic and chromatin immunoprecipitation analyses that allow to map the genomic distribution of RNAPII and TEFs as well as the efficiency of mRNA synthesis. The combined analysis of these datasets will provide novel insight into the action of TEFs under stress conditions and how they contribute to plant tolerance to environmental stress, which is also relevant in the light of progressing climate change.

• DFG Programme: Research Grants