CAREER: Engineering genome topology to attenuate pathologic short tandem repeat instability

DNA序列存储信息，并且对这些信息的访问在许多层面上受到控制。分散在DNA上的是随机的重复序列，称为短串联重复序列（STR）。STR有助于调节基因表达，也可以在长度上扩展和收缩。STR的过度扩增可导致许多疾病，包括ALS（卢伽雷氏病）、阿尔茨海默氏症和亨廷顿氏病。该项目将重点关注是什么原因导致STR扩增导致疾病。适当应用统计和计算工具是在这方面取得进展的关键。一个培训项目将为学生提供学习这些技术的机会。关于转录因子和表观遗传标记如何在线性基因组的背景下调节大脑中的神经突触，我们已经知道了很多。然而，我们理解神经系统疾病如脆性X综合征（FXS）、亨廷顿病和阿尔茨海默病中突触严重破坏的机制的能力仍然存在严重的局限性。最近，Cremins实验室发现，几乎所有的疾病相关STR（daSTR）都位于划分基因组折叠模式的边界，称为拓扑关联结构域（topologically associated domain，简称STR）。该实验室继续发现，FXS中的神经元边界被严重破坏，从而揭示了遗传序列的高阶折叠作为理解具有突触缺陷的神经系统疾病的新维度。一个根本的未解决问题是为什么一些STR容易发生病理性扩张，而人类基因组中数十万个重复片段却相对稳定。本项目的总体目标是了解结构蛋白CTCF的占用率和STR不稳定性之间的机械联系。我们的中心假设是，具有超高CTCF密度的边界代表了人类基因组中易受不稳定性影响的热点。为了验证这一假设，我们提出了实验和计算研究，以（1）定量测量CTCF密度和双链断裂对STR不稳定性的作用，（2）工程CTCF占用，以诱导STR expandation.This奖项的功能变化反映了NSF的法定使命，并已被认为是值得通过评估使用基金会的智力价值和更广泛的影响审查标准的支持。

DNA sequences store information, and access to this information is controlled at many levels. Scattered across DNA are random, repeated sequences referred to as short tandem repeats (STRs). STRs help regulate gene expression and can also expand and contract in length. Overexpansion of STR's can lead to a number of diseases, including ALS (Lou Gehrig’s disease), Alzheimer’s, and Huntington’s. This project will focus on what causes STR expansion that leads to disease. The proper application of statistics and computational tools are key to making progress in this effort. A training program will provide students with the opportunity to learn those techniques.Much is already known regarding how transcription factors and epigenetic marks work in the context of the linear genome to regulate neural synapses in the brain. Yet, severe limitations still exist in our ability to understand the mechanisms by which synapses are severely disrupted in neurological disorders such as fragile X syndrome (FXS), Huntington’s disease, and Alzheimer’s disease. Recently, the Cremins lab discovered that nearly all disease-associated STRs (daSTRs) are located at boundaries demarcating a genome folding pattern termed the topologically associating domain (TAD). The lab went on to discover that TAD boundaries are severely disrupted in FXS, thus revealing higher-order folding of the genetic sequence as a new dimension in understanding neurological disorders with synaptic defects. A fundamental unresolved question is why some STRs are susceptible to pathologic expansion, whereas hundreds of thousands of repeat tracts across the human genome are relatively stable. The overall objective of this project is to understand the mechanistic link between occupancy of the architectural protein CTCF and STR instability at TAD boundaries. Our central hypothesis is that TAD boundaries with ultra-high CTCF density represent hotspots in the human genome susceptible to instability. To test this hypothesis, we propose experimental and computational studies to (1) quantitatively measure the role for CTCF density and double strand breaks on STR instability and (2) engineer CTCF occupancy to induce a functional change in STR expansion.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.