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具有不可或缺的作用，这种结构的破坏可能导致基因表达的异常模式，对生物体造成严重后果。可形成异常结构的高度重复DNA序列的存在与遗传疾病有关，遗传疾病是正常调控丧失的结果。该项目旨在了解这些缺陷如何影响DNA的组织，以及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专业学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的入门物理实验室序列开发一个以研究为导向的课程，启动研究研讨会作为芝加哥地区社区学院的推广，并支持有前途的研究人员的学士后培训计划。该项目旨在提供强调跨学科学习的实质性学习经验，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）遗传性疾病中的发现越来越多。疾病相关的STR序列具有形成非螺旋结构的强烈倾向，所述非螺旋结构作为双链DNA（dsDNA）中的缺陷而出现。虽然大量的工作已经致力于涉及这些序列的遗传过程，它们的相关结构对基因组的三维结构提出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，以实验方式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则。第一个目标将表征两种类型的缺陷：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表征的缺陷插入到较大的DNA结构域中，以检查dsDNA折叠的两个方面：i）短程环形成和ii）大规模超螺旋动力学。该项目的发现将告知DNA水平上的局部结构缺陷如何诱导基因组错误折叠。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NSF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.