Trinucleotide repeat disorders and the 3D genome

三核苷酸重复紊乱和 3D 基因组

• 批准号: 10025381
• 负责人: Linda Zhou
• 金额: $ 3.26万
• 依托单位: UNIVERSITY OF PENNSYLVANIA
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-09-01 至 2022-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10025381
• 关键词: 3-Dimensional; Ablation; Address; Affect; Alleles; Anxiety; Architecture; Binding; Cataract; Cell Line; Cells; Chromatin; Complex; DNA Sequence; Data; Defect; Dimensions; Disease; Endonuclease I; Engineering; Epigenetic Process; Evolution; FMR1; Fragile X Syndrome; Friedreich Ataxia; Functional disorder; Gene Expression; Genes; Genetic; Genetic Transcription; Genome; Genome engineering; Heart Abnormalities; Human; Hyperactive behavior; Individual; Inherited; Lead; Length; Light; Link; Location; Maps; Measures; Mediating; Molecular; Mutate; Myotonic Dystrophy; Outcome; Patients; Phenotype; Quantitative Reverse Transcriptase PCR; Repetitive Sequence; Resolution; Role; Seizures; Series; Severity of illness; Short Tandem Repeat; Site; Structure; Sum; Symptoms; Testing; Therapeutic Intervention; Trinucleotide Repeat Expansion; Trinucleotide Repeats; Work; attenuation; base; causal variant; experimental study; genome editing; induced pluripotent stem cell; insight; novel therapeutic intervention; prevent; recruit; respiratory; social deficits; targeted treatment; therapeutic target; therapy development

Project Summary Unstable expansion of repetitive DNA sequences termed short tandem repeats (STRs) serves as the mechanistic basis for more than 25 inherited human disorders. Patients with unstable repeat expansion diseases suffer from a complex array of symptoms, including: cardiac defects, cataracts, anxiety, hyperactivity, low IQ, social deficits, respiratory defects and seizures. In some diseases, such as Fragile X Syndrome and Freidreich’s Ataxia, the downstream phenotype is mediated in large part by reduced gene expression. In all of these diseases, continuous repeat expansion is associated with disease severity. Treating trinucleotide repeat disorders is thus complex because the primary effectors of disease include both the continuous expansion of repetitive sequences as well as disrupted expression of the gene containing the repeat. Thus, an increased understanding of the molecular mechanisms governing STR instability and expansion related gene dysregulation would facilitate efforts to develop therapies to prevent and treat repeat expansion disorders. In our preliminary work, we introduce the higher order chromatin architecture as a new dimension in understanding these features in repeat expansion disorders. Our data shows that (1) the large majority of disease associated STRs are located precisely at boundaries demarcating 3D genome folding domains termed topologically associating domains (TADs) and subTADs and (2) repeat expansion in the FMR1 gene, the genetic driver for Fragile X Syndrome, results in CTCF occupancy ablation and large-scale TAD/subTAD reorganization in a manner that correlates with STR tract length, disease severity, and transcriptional disruption of FMR1. Given the increasing importance of the 3D genome, there is a critical need to extend our preliminary data to understand how the 3D genome may be perturbed by trinucleotide repeat expansion and whether this perturbation could contribute to the primary effectors of disease originating from the causal gene itself: repeat instability and dysregulated gene expression. This proposal outlines the next steps doing so. In the first aim, I will perform genome engineering experiments to determine if the domain reorganization we have observed around FMR1 contributes to decreased gene expression. In the second aim, I will create high resolution topological maps around the FXN gene, the genetic driver for Freidreich’s ataxia, the determine whether boundary disruption is present in an additional trinucleotide repeat disorder. In the third aim, I will perform additional genome editing experiments to elucidate whether domain boundary disruptions can influence repeat instability and gene expression of the FXN gene. In sum, the accomplishment of these aims would demonstrate that the 3D genome can be perturbed in repeat expansion disorders and that this perturbation can mediate repeat instability and disrupted gene expression. Ultimately, we could use these results to determine whether manipulating the 3D genome could be a potential therapeutic target for treating these diseases.

项目摘要 重复的DNA序列的不稳定膨胀称为短串联重复序列（STR）作为 超过25种遗传性人类疾病的机械基础。重复不稳定的患者 疾病患有复杂的症状，包括：心脏缺陷，白内障，动画，多动症， 智商低下，社会缺陷，呼吸缺陷和癫痫发作。在某些疾病中，例如脆弱的X综合征和 Freidreich的共济失调，下游表型在很大程度上是通过降低的基因表达介导的。总的来说 这些疾病，连续重复扩张与疾病的严重程度有关。处理三核苷酸重复 因此，疾病很复杂，因为疾病的主要作用包括连续扩张 重复序列以及包含重复的基因的表达。那增加了 理解有关Str不稳定性和膨胀相关基因的分子机制 失调将有助于开发预防和治疗重复扩张障碍的疗法。 在我们的初步工作中，我们介绍了高阶染色质体系结构作为新的维度 在重复扩展障碍中了解这些功能。我们的数据表明（1）绝大多数疾病 相关的strs精确地位于划分3D基因组折叠域的边界 拓扑关联域（TADS）和tads和（2）在FMR1基因中重复扩展，遗传 易碎X综合征的驱动器，导致CTCF占用消融和大规模TAD/SUBTAD重组 以与Str段的长度，疾病严重程度和FMR1的转录破坏相关的方式。 鉴于3D基因组的重要性越来越重要，因此将我们的初步数据扩展到 了解如何通过三核苷酸重复扩展来扰动3D基因组以及是否存在 扰动可能导致因果基因本身起源的疾病的主要作用：重复 不稳定性和失调的基因表达。该建议概述了这样做的下一步。在第一个目标中，我 将执行基因组工程实验，以确定我们观察到的域是否重组 FMR1附近有助于降低基因表达。在第二个目标中，我将创建高分辨率 FXN基因周围的拓扑图是Freidreich共济失调的遗传驱动器，该基因确定是否确定是否确定 边界破坏在另外的三核苷酸重复障碍中呈现。在第三个目标中，我会表演 其他基因组编辑实验以阐明域边界是否会影响重复 FXN基因的不稳定性和基因表达。总而言之，这些目标的成就将证明 3D基因组可以在重复膨胀障碍中受到干扰，并且这种扰动可以介导 重复不稳定性并破坏基因表达。最终，我们可以使用这些结果来确定是否 操纵3D基因组可能是治疗这些疾病的潜在治疗靶点。