Trinucleotide repeat disorders and the 3D genome

三核苷酸重复紊乱和 3D 基因组

基本信息

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
项目类别：
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

项目摘要

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种遗传性疾病的机械基础。疾病患有一系列症状，包括：心脏缺陷，白内拉伤，焦虑，多动症，智商低，社会缺陷，呼吸缺陷和癫痫发作。 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这些疾病，连续重复的扩张与疾病的严重程度有关因此疾病很复杂，因为疾病的主要效应因子包括连续扩张重复的序列为-as -as -as -discupt的基因表达，含有重复。了解有关strrea和扩展相关基因的分子机制脱症将有助于开发治疗治疗疗法扩张障碍的疗法的努力。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了解重复扩张障碍中的植物。相关的strs精确地位于划分3D基因组折叠域的边界 FMR1基因中的拓扑关联域（TADS）和tads和（2）重复扩展易碎X综合征的驱动器，导致CTCF占用量和大规模TAD/SUBTAD重组以与链长，疾病严重程度和FMR1转录相关的方式。鉴于3D基因组的重要性越来越大了解如何重复重复3D基因组以及是否扰动可能有助于起源于因果基因本身的疾病的主要效应因素：重复不稳定性和失调的基因表达。将执行基因组工程实验，以确定我们观察到的域是否重新化 FMR1左右有助于下降的基因表达。 FXN基因周围的拓扑图是Freidreich'Staxia的遗传驱动器，确定是否确定边界破坏存在于三核苷酸重复障碍中。其他基因组编辑实验，以阐明Doumain边界是否会影响重复 FXN基因的不稳定性和基因表达。 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性和基因表达中断。操纵3D基因组可能是治疗这些疾病的潜在治疗靶点。