EAPSI: Exploring 3-D DNA Organization and Evolution in a Microbial Eukaryote

Maurer-Alcala Xyrus X, Northampton MA

Investigators

Abstract

Over the last few decades, our understanding of how DNA is organized in the nucleus has evolved from a ?sack? full of chromosomes to a highly ordered structure. Despite the growing evidence for conserved and adaptive patterns in how the genome is organized in the nucleus, there are few studies exploring the relationship of genome evolution and its organization in 3-dimensions. This is partly due to the way that genome evolution is currently perceived, where genomic sequences are treated as long linear molecules rather than the highly folded chromosomes that actually exist inside the eukaryotic cell. In collaboration with Dr. Meng-Chao Yao, at Academia Sinica, this project will work with Tokophrya sp. (an unusual microbial eukaryote with ?gene-sized? chromosomes and a complex life cycle) as the study organism to explore patterns of evolution and how evolution is reflected in its nuclear architecture. Currently, there are few studies exploring the evolution of the eukaryotic genome beyond its sequence. Through the use of molecular tools such as qPCR and fluorescence in situ hybridization, the project will be able to estimate the actual abundance of different ?gene-sized? chromosomes, their relative expression, and their position as well. Coupling these physical properties of Tokophrya with bioinformatic approaches to explore patterns of molecular evolution such as pairwise distances and codon bias will provide the basis for a strong comparative study. Previous work in microbial eukaryotes has helped to demonstrate some ?universal? patterns in nuclear architecture, such as the organization of DNA into DNA rich regions surrounding DNA poor corridors. Further work with divergent organisms such as Tokophrya sp. will provide intimate details about relationship between molecular evolution and how evolutionary forces participate in the non-random organization of the 3-dimensional genome. This award under the East Asia and Pacific Summer Institutes program supports summer research by a U.S. graduate student and is jointly funded by NSF and the Ministry of Science and Technology of Taiwan.