Selfish DNA elements—such as plasmids or virus episomes that are present in a wide range of organisms—utilize strategies to ensure their transmission to the next generation, without benefit or detriment to the host organism. One strategy utilized by a plasmid present in budding yeast is to attach itself to the host chromosomes and “hitchhike†to daughter cells within a growing cell population. Research supported by this project will map the chromosomal locations where one such yeast plasmid attaches, and then characterize the plasmid and host factors that contribute to hitchhiking. The experimental approaches will utilize current genome-wide methodologies that will be performed by post-doctoral fellows, graduate students, undergraduate students and high-school seniors (as summer trainees). The findings from this study will be incorporated into 4-5 lectures on Selfish DNA that will form part of an upper division undergraduate course and a first year graduate course. Some of the experiments will be carried out under the Freshmen Research Initiative Program at UT Austin. Through the ‘UT Austin Community Outreach,’ High School seniors from urban areas of minority and low socioeconomic status will also participate in a program of supervised research. In coordination with UTeach Outreach Institute, a learning module on ‘Selfishness of Genes and Genomes’ designed to awaken scientific curiosity among middle and high school students will be developed. Overall, this scientific undertaking is expected to have far-reaching societal impact by advancing basic science, developing new technologies and contributing to human health.
Current evidence suggests that the partitioning system of the yeast 2-micron plasmid tethers plasmid sisters formed by replication to sister chromatids, enabling their chromosome-like 1:1 segregation. Yet direct proof of this hitchhiking model is lacking. According to the investigator's working hypothesis, interactions between plasmid partitioning proteins and host chromatin binding proteins are responsible for plasmid localization to chromosomal loci. The researchers will identify and characterize plasmid tethering sites on chromosomes by two independent but complementary high-throughput approaches: ChIP-seq and 4C-seq. The expectation is that there will be considerable overlap between DNA sequences enriched by the two methods. By refining the data from the two approaches using multiple controls, and by filtering the data sets from one against the other, the investigators will be able to define authentic plasmid tethering sites on chromosomes with high confidence. They will then test how tethering efficiency and plasmid stability are affected by mutational inactivation of a number of plasmid and host proteins that are implicated in tethering. This study will provide the most rigorous test of the hitchhiking model for plasmid segregation and will impact a model for the convergent evolution of chromosome-coupled survival strategies among selfish DNA elements as diverse as the yeast plasmid and mammalian viruses. It will thus shed new light on the mechanistic understanding of the shared lifestyles of selfish DNA elements that inhabit evolutionarily distant hosts. It will also help design simple, effective and innovative strategies for maintaining beneficial extra-chromosomal elements in eukaryotic host cells and for eliminating harmful elements.
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.
