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 被称为短串联重复序列（STR）的重复DNA序列的不稳定扩增充当了 超过25种遗传性人类疾病的机制基础。重复扩张不稳定的患者 疾病具有一系列复杂的症状，包括：心脏缺陷、白内障、焦虑、多动症， 低智商社交缺陷呼吸缺陷和癫痫在某些疾病中，如脆性X综合征和 Freidreich共济失调，下游表型在很大程度上是由基因表达减少介导的。在所有 在这些疾病中，持续的重复扩增与疾病的严重程度相关。治疗三核苷酸重复 因此，疾病是复杂的，因为疾病的主要效应包括持续的扩张， 重复序列以及含有该重复序列的基因的表达被破坏。因此， 理解STR不稳定性和扩增相关基因的分子机制 调节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，我们引入了更高级的染色质结构作为一个新的维度， 理解重复扩增障碍的这些特征。我们的数据显示，（1）大多数疾病 相关的STR精确地位于划分3D基因组折叠结构域的边界， 拓扑关联结构域（TADs）和subTADs，以及（2）FMR 1基因中的重复扩增， 脆性X综合征的驱动因素，导致CTCF占用消融和大规模的骨/皮下组织重组 与STR序列长度、疾病严重程度和FMR 1转录破坏相关。 鉴于3D基因组的重要性日益增加，迫切需要将我们的初步数据扩展到 了解三维基因组如何被三核苷酸重复扩增所干扰，以及这是否 干扰可能有助于疾病的主要效应源来自致病基因本身：重复 不稳定和基因表达失调。本提案概述了今后的步骤。在第一个目标中，我 将进行基因组工程实验，以确定我们观察到的结构域重组是否 FMR 1周围的基因表达减少。在第二个目标中，我将创建高分辨率 FXN基因周围的拓扑图，Freidreich共济失调的遗传驱动因素，决定了是否 边界破坏存在于另外的三核苷酸重复紊乱中。在第三个目标中， 额外的基因组编辑实验，以阐明域边界破坏是否会影响重复 FXN基因的不稳定性和基因表达。总之，这些目标的实现将表明， 3D基因组可以在重复扩增障碍中受到干扰，并且这种干扰可以介导 重复不稳定性和基因表达中断。最终，我们可以用这些结果来确定 操纵3D基因组可能是治疗这些疾病的潜在治疗靶点。