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

EAPSI：探索微生物真核生物中的 3D DNA 组织和进化

• 批准号: 1614219
• 负责人: Xyrus Maurer-Alcala
• 金额: $ 0.54万
• 依托单位: Maurer-Alcala Xyrus X
• 依托单位国家: 美国
• 项目类别: Fellowship Award
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-06-15 至 2017-05-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1614219&HistoricalAwards=false
• 关键词: EAPSI; Exploring; DNA; Organization; Evolution

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.

在过去的几十年里，我们对DNA在细胞核中是如何组织的理解已经从一个？sack？充满了染色体的高度有序的结构。尽管越来越多的证据表明基因组在细胞核中的组织方式是保守的和适应性的，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看法，基因组序列被视为长的线性分子，而不是实际存在于真核细胞内的高度折叠的染色体。在与姚孟超博士合作，在中央研究院，这个项目将与Tokophrya sp。（一个不寻常的微生物真核生物与？基因大小？染色体和复杂的生命周期）作为研究生物体来探索进化模式以及进化如何反映在其核结构中。目前，很少有研究探索真核基因组序列以外的进化。通过使用分子工具，如qPCR和荧光原位杂交，该项目将能够估计不同的实际丰度？基因大小？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，以探索分子进化模式，如成对距离和密码子偏好，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有助于证明一些？通用的？核结构的模式，如DNA组织成DNA丰富的区域周围的DNA穷人走廊。对不同生物如Tokophrya sp.的进一步研究将提供有关分子进化与进化力量如何参与三维基因组非随机组织之间关系的详细信息。该奖项在东亚和太平洋夏季研究所计划下支持美国研究生的夏季研究，由NSF和台湾科技部共同资助。