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

在过去的几十年里，我们对DNA如何在细胞核中组织的理解是从一个“麻袋”进化而来的。充满了染色体，形成了高度有序的结构。尽管越来越多的证据表明基因组是如何在细胞核中组织的保守和适应性模式，但很少有研究探索基因组进化与其三维组织的关系。这部分是由于目前对基因组进化的认知方式，基因组序列被视为长线性分子，而不是真核细胞内实际存在的高度折叠的染色体。该项目与中国科学院姚孟超博士合作，将与Tokophrya sp.(一种不寻常的微生物真核生物，基因大小为？染色体和一个复杂的生命周期)作为研究生物体探索进化模式和进化是如何反映在其核结构。目前，对真核生物基因组序列以外的进化进行探索的研究很少。通过使用qPCR和荧光原位杂交等分子工具，该项目将能够估计不同基因大小的实际丰度。染色体，它们的相对表达，以及它们的位置。将Tokophrya的这些物理特性与生物信息学方法相结合，探索分子进化模式，如成对距离和密码子偏倚，将为强有力的比较研究提供基础。以前在微生物真核生物方面的工作已经帮助证明了一些普遍的？核结构的模式，例如DNA组织进入DNA丰富区域周围的DNA贫乏走廊。对Tokophrya等不同生物的进一步研究将提供分子进化之间关系的详细信息，以及进化力量如何参与三维基因组的非随机组织。该奖项隶属于东亚及太平洋暑期研究所项目，由美国国家科学基金会和台湾科技部共同资助，支持美国研究生的暑期研究。

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.