Negative transcription elongation factors prevent transcriptional interference in plants

植物和动物的基因组可以包含数以万计的基因，每一个基因都必须在特定的水平、时间和位置开启或表达。一个根本性的挑战是确保一个基因的表达不会不适当地影响其邻近基因的表达。在植物中，人们对如何防止这种干扰知之甚少，研究这种机制是本项目的目标。这项研究将由本科生和研究生进行，项目中产生的数据将用于高中教师的在线分子遗传学和基因组学课程，以帮助他们获得可以在课堂上使用的新技能。当两个基因靠近位于同一条DNA链上，即串联时，有可能通过RNA聚合酶II （Pol II）转录表达，从而干扰下游基因的表达。防止这种干扰的一种方法是在Pol II接近第一个基因末端时阻止其前进，从而阻止第二个基因启动子区域的入侵。初步工作导致发现一个家族的负转录延伸因子，称为边界蛋白，是串联基因之间的富集区域。BORDER蛋白似乎通过促进上游基因末端附近Pol II的暂停来防止表达干扰。在缺乏BORDER蛋白的情况下，上游基因的停顿减少，Pol II进入下游基因的启动子区域，导致其表达减少。实验将研究BORDER蛋白如何与Pol II相互作用以诱导暂停。研究将在拟南芥和水稻两种植物物种中进行，这两种植物都有BORDER蛋白，但串联基因之间的间距不同。这种比较方法将有助于辨别跨物种的BORDER蛋白功能的共同特征。此外，由于真菌和动物中也存在与植物BORDER蛋白相似的蛋白质，因此该研究有望对理解串联排列基因的表达如何协调产生广泛影响。这项研究是由分子和细胞生物科学部的生物科学理事会遗传机制计划和综合有机系统部的植物基因组研究计划共同资助的。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

The genomes of plants and animals can contain tens of thousands of genes, each of which must be turned on, or expressed, at specific levels, times, and locations. A fundamental challenge is ensuring that the expression of one gene does not inappropriately affect the expression of its neighbors. In plants, little is known about how such interference is prevented, and studying this mechanism is the goal of this project. The research will be carried out by undergraduate and graduate students, and the data generated in the project will be used in an online Molecular Genetics and Genomics course for high school teachers to help them gain new skills that they can take to their classrooms. When two genes are located close together on the same strand of DNA, i.e., in tandem, there is potential for expression--transcription by RNA polymerase II (Pol II)--to interfere with expression of the downstream gene. One way to prevent this interference would be to block the progress of the Pol II as it nears the end of the first gene, so that invasion of the promoter region of the second gene is barred. Preliminary work led to discovery of a family of negative transcription elongation factors, called BORDER proteins, that are enriched regions between tandem genes. The BORDER proteins appear prevent expression interference by promoting pausing of Pol II near the end of the upstream gene. In the absence of BORDER proteins, pausing in the upstream gene is reduced and Pol II moves into the promoter region of the downstream gene, resulting in its decreased expression. Experiments will study how the BORDER proteins interact with Pol II to induce pausing. Studies will be conducted in two plant species, Arabidopsis and rice, which both have BORDER proteins, but different spacing between tandem genes. This comparative approach will help discern the shared features of BORDER protein function across species. Moreover, because proteins with similarities to the plant BORDER proteins exist also in fungi and animals, the work is expected to have broad impact on understanding how expression of tandemly arranged genes is coordinated.This research is co-funded by the Biological Sciences Directorate Genetic Mechanisms Program in the Division of Molecular and Cellular Biosciences and the Plant Genome Research Program in the Division of Integrative Organismal Systems.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.