CAREER: I. The local and global effects on genomic architecture by defects induced in repetitive DNA domains and II. Development of integrative curriculum in physics

基因组的三维排列在其信息内容的调节中起着不可或缺的作用，这种结构的破坏可能导致基因表达模式异常，对生物体造成严重后果。可以形成异常结构的高度重复DNA序列的存在与遗传疾病有关，遗传疾病是失去正常调节控制的结果。该项目旨在了解这些缺陷如何影响DNA的组织，从而了解这些缺陷如何导致与某些遗传疾病相关的有害蛋白质表达模式。这项工作的教育部分解决了提高本科理科生的核心科学能力和扩大获得研究经验的需要。该项目将为芝加哥洛约拉大学（Loyola University Chicago）的入门物理实验室序列开发一套研究型课程，启动研究研讨会，向芝加哥地区的社区学院推广，并为有前途的研究人员提供学士学位后培训计划。该项目旨在提供实质性的学习经验，强调跨学科学习，扩大STEM研究中代表性不足的群体的机会，并提高有前途的学生对STEM职业的职业准备。基因组错误折叠在短串联重复序列（STR）遗传疾病中被越来越多地发现。与疾病相关的STR序列具有形成非螺旋结构的强烈倾向，这种结构在双链DNA （dsDNA）中出现缺陷。尽管大量的工作已经投入到涉及这些序列的遗传过程中，但它们的相关结构对基因组三维结构的拓扑挑战在很大程度上仍然未知。该项目将利用单分子荧光和互补的生化策略，通过实验量化不同序列和类型的结构缺陷如何改变dsDNA的机械特性，并影响引导其形成大环和更复杂结构的折叠原理。第一个目标将描述两种类型的缺陷：同源DNA内环和由三核苷酸重复序列（CXG）N组成的疾病相关STR结构。第二个目标将集中于将特征缺陷插入到更大的DNA结构域中，以检查dsDNA折叠的两个方面：i)短距离环形成和ii)大规模，超卷曲动力学。该项目的研究结果将揭示DNA水平上的局部结构缺陷是如何诱导基因组错误折叠的。该奖项由分子和细胞生物科学的分子生物物理学和遗传机制集群支持。该奖项反映了美国国家科学基金会的法定使命，并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，被认为值得支持。

The three-dimensional arrangement of the genome has an integral role in the regulation of its information content, and disruption of this architecture can lead to abnormal patterns of gene expression with grave consequences for the organism. The presence of highly repetitive DNA sequences that can form aberrant structures has been linked to genetic diseases which are a result of a loss of normal regulatory controls. The project seeks to understand how these defects influence the organization of DNA, and thus how these defects might lead to the deleterious protein expression patterns associated with some genetic diseases. The educational component of the work addresses the need to enhance the core scientific competencies of undergraduate science majors and expand access to research experiences. The project will develop a research-oriented curriculum for the introductory physics lab sequence at Loyola University Chicago, initiate research workshops as outreach to Chicago-area community colleges and support a post-baccalaureate training program for promising researchers. The project seeks to provide substantive learning experiences that emphasize interdisciplinary learning, expand opportunities for underrepresented groups in STEM research, and improve the career readiness of promising students for STEM careers.Genomic misfolding has been increasingly identified in short tandem repeat (STR) genetic disorders. Disease-related, STR sequences have a strong propensity to form non-helical structures that arise as defects in double-stranded DNA (dsDNA). Although significant work has been devoted to genetic processes that involve these sequences, the topological challenges that their associated structures present to the three-dimensional architecture of the genome remain largely unknown. The project will utilize single-molecule fluorescence and complementary biochemical strategies to quantify experimentally how different sequences and types of structural defects alter the mechanical properties of dsDNA and affect the folding principles that guide its formation into large loops and more complex structures. The first aim will characterize two types of defects: homologous DNA internal loops and disease-relevant STR structures consisting of the trinucleotide repeat sequence (CXG)N. The second aim will focus on the insertion of the characterized defects into larger DNA domains to examine two aspects of dsDNA folding: i) short-range loop formation and ii) large-scale, supercoiling dynamics. The findings from the project will inform how local structural defects at the DNA level can induce genomic misfolding. This award is supported by the Molecular Biophysics and Genetic Mechanisms clusters of Molecular and Cellular Biosciences.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.