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

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The genomic DNA of eukaryotic organisms is packaged into a nucleoprotein structure termed chromatin, and nucleosome particles represent the basic unit of chromatin. Hence, by restricting the accessibility of DNA nucleosomes repress various DNA-dependent processes such as 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 of DNA templates assembled into nucleosomes. 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 modulating various stages of development.Using the Arabidopsis plant model, we have recently started investigating the involvement of TEFs in plant responses to environmental cues. Our preliminary analyses revealed that compared to controls, mutant plants deficient in certain TEFs exhibited distinct defects in their response to stressful conditions. Changing circumstances require (relatively rapid) transcriptional reprogramming that apparently is especially demanding for the RNAPII elongation machinery. Therefore, we propose provoking transcriptional reprogramming induced by environmental stress as a tool to study the functionality of TEFs in a meaningful biological context. We intend to assay mutants deficient in various TEFs upon exposure to a set of stress conditions (e.g. heat, cold, drought) to challenge RNAPII elongation. Employing genome-wide analyses (transcriptomics, chromatin immunoprecipitation in combination with nucleosome position/stability assays) we intend to characterise the molecular contribution of different TEFs in plant responses to abiotic stress conditions. In conclusion, the proposed project will provide novel insight into the action of TEFs in transcriptional reprogramming. Beyond that it will complement a more complete understanding of plant responses to environmental stress, which is also relevant in the light of progressing climate change.