The role of factors regulating transcript elongation by RNA polymerase II in tuning plant gene expression programs

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有助于精确调节细胞转录物水平。我们之前对拟南芥植物模型的各种tef进行了表征，表明缺乏某些tef的突变植物在生长和发育中表现出明显的缺陷。对于与伸长RNAPII形成转录延伸复合体相关的tef之间的功能相互作用知之甚少。我们将分析缺乏不同tef对的双突变植物，以研究它们在分子水平上的合作（招募，功能相互依赖）。有趣的是，只有特定基因亚群的表达受到某些tef缺失带来的伸长缺陷的损害。利用全基因组分析（转录组学，染色质免疫沉淀），我们打算确定目标基因的特征，这些特征决定了TEF作用的要求，以实现有效的转录。构建转录延伸报告结构将为tef在植物中的作用机制提供进一步的线索。总之，该项目将为TEF在体内RNAPII转录过程中的作用及其在建立正确植物发育所需的精确基因表达谱中的作用提供新的见解。

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.We have previously characterised various TEFs of the Arabidopsis plant model demonstrating that mutant plants deficient in certain TEFs display distinct defects in growth and development. Not much is known about functional interactions between TEFs that associate with elongating RNAPII forming the transcript elongation complex. We will analyse double-mutant plants lacking different pairs of TEFs to examine their cooperation on the molecular level (recruitment, functional interdependence). Interestingly, only the expression of specific subsets of genes is impaired by the elongation defects brought about by the absence of certain TEFs. Employing genome-wide analyses (transcriptomics, chromatin immunoprecipitation) we intend to identify features of target genes that determine the requirement for TEF action to achieve efficient transcription. Establishing a transcript elongation reporter construct will yield further clues about the mechanism of action of TEFs in planta. In conclusion, the proposed project will provide novel insight into TEF action during RNAPII transcription in vivo and their role in establishing precise gene expression profiles required for proper plant development.