CAREER: Exploring nucleosome-depleted sequences for novel applications in synthetic biology

职业：探索核小体耗尽序列在合成生物学中的新应用

• 批准号: 1749782
• 负责人: Zengyi Shao
• 金额: $ 55.12万
• 依托单位: Iowa State University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-03-15 至 2025-02-28
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1749782&HistoricalAwards=false
• 关键词: CAREER; Exploring; nucleosome; depleted; sequences

Fully understanding how chromosomes affect cell behavior is important to many applications in biotechnology and improving human health. Many DNA segments that were previously thought to be just filler, or "junk" DNA, have recently been discovered to influence the cell metabolism in important ways. This project will study the influence of a specific subgroup of these segments on cell behavior. In addition, the principal investigator will develop a uniquely-structured undergraduate research program. She will also mentor next-generation STEM (science, technology, engineering and mathematics) teachers, and promote the participation of underrepresented minorities and persons with disabilities in STEM fields. When completed, this project will have developed new molecular tools for harnessing the power of biological systems to produce important products, and helped encourage and prepare highly-skilled students with diverse backgrounds to engage in STEM careers. This proposal addresses the low orthogonality that is frequently encountered between well-characterized biological components and genetic contexts. The canonical Design-Build-Test-Learn cycle dissects natural complex biological subjects into distinct functional parts through a "subtraction" hierarchy. However, the interplay among multiple layers in new combinations brings about unwanted design imprecision. Selecting three distinct yeast species as testbeds, the principal investigator will systematically characterize the highly exposed nucleosome-depleted genomic regions and create synthetic insulators to counteract genetic context influence on heterologous gene and pathway expression. The concept of insulating transcriptional elements to create designed regions that regulate gene expression with high orthogonality has been applied with some success in bacterial genetic circuits. Efforts in yeast systems, with a higher degree of complexity, are very limited. The highly exposed nucleosome-depleted regions will be further exploited to address lack of stable episomal plasmids faced by many nonconventional yeasts.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.

充分了解染色体如何影响细胞行为对生物技术的许多应用和改善人类健康至关重要。 许多以前被认为只是填充物或“垃圾”DNA的DNA片段，最近被发现以重要的方式影响细胞代谢。本项目将研究这些片段的特定亚组对细胞行为的影响。 此外，首席研究员将制定一个结构合理的本科研究计划。她还将指导下一代STEM（科学，技术，工程和数学）教师，并促进代表性不足的少数民族和残疾人参与STEM领域。完成后，该项目将开发新的分子工具，利用生物系统的力量生产重要产品，并帮助鼓励和准备具有不同背景的高技能学生从事STEM职业。这一建议解决了低正交性，经常遇到的良好表征的生物成分和遗传背景之间。 规范的设计-构建-测试-学习循环通过“减法”层次结构将自然复杂的生物主题分解为不同的功能部分。然而，新组合中多层之间的相互作用带来了不必要的设计不精确性。 选择三种不同的酵母物种作为试验平台，主要研究者将系统地表征高度暴露的核小体耗尽的基因组区域，并创建合成绝缘体，以抵消遗传背景对异源基因和途径表达的影响。 隔离转录元件以产生具有高正交性的调节基因表达的设计区域的概念已经在细菌遗传电路中取得了一些成功。 在酵母系统中的努力，具有较高程度的复杂性，是非常有限的。 高度暴露的核小体耗尽区域将被进一步利用，以解决许多非传统酵母面临的稳定游离质粒缺乏的问题。该奖项反映了NSF的法定使命，并被认为值得通过使用基金会的知识价值和更广泛的影响审查标准进行评估来支持。

项目成果

Revisiting the unique structure of autonomously replicating sequences in Yarrowia lipolytica and its role in pathway engineering

• DOI: 10.1007/s00253-021-11399-4
• 发表时间: 2021-08
• 期刊: Applied Microbiology and Biotechnology
• 影响因子: 5
• 作者: C. Lopez;Mingfeng Cao;Zhanyi Yao;Zengyi Shao