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

真核生物的基因组DNA被包装成称为染色质的核蛋白结构，核小体颗粒代表染色质的基本单位。因此，通过限制DNA的可及性，核小体抑制各种DNA依赖的过程，如基因转录。因此，转录蛋白质编码基因（合成mrna）的RNA聚合酶II （RNAPII）需要不同的辅助因子，以促进组装成核小体的DNA模板的有效转录延伸。在促进RNAPII转录延伸期的蛋白质中，有所谓的转录延伸因子（transcript伸长factor， tef）。它们代表了一组具有不同功能的异质蛋白质，包括调节RNAPII的催化特性或破坏酶路径中的核小体的稳定性，从而实现有效的mRNA合成。与其在基因转录中的功能一致，tef有助于准确调节细胞转录物水平，从而调节发育的各个阶段。利用拟南芥植物模型，我们最近开始研究tef在植物对环境线索的反应中的作用。我们的初步分析显示，与对照相比，缺乏某些TEFs的突变植株在对应激条件的反应中表现出明显的缺陷。不断变化的环境需要（相对快速的）转录重编程，这显然对RNAPII延伸机制的要求特别高。因此，我们提出在有意义的生物学背景下，激发环境应激诱导的转录重编程作为研究tef功能的工具。我们打算在暴露于一系列胁迫条件（如热、冷、干旱）以挑战RNAPII伸长时检测各种tef缺陷的突变体。利用全基因组分析（转录组学、染色质免疫沉淀结合核小体位置/稳定性分析），我们打算描述不同tef在植物对非生物胁迫条件的反应中的分子贡献。总之，该项目将为tef在转录重编程中的作用提供新的见解。除此之外，它还将补充更全面地了解植物对环境胁迫的反应，这也与不断发展的气候变化有关。

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.