Negative transcription elongation factors prevent transcriptional interference in plants

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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.