The Effects of Physical Disruption on Genome Organization and Integrity

物理破坏对基因组组织和完整性的影响

• 批准号: 8256197
• 负责人: Rachel Patton McCord
• 金额: $ 4.92万
• 依托单位: UNIV OF MASSACHUSETTS MED SCH WORCESTER
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-02-01 至 2014-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8256197
• 关键词: Affect; B-Lymphocytes; Biological Process; Caliber; Cataloging; Catalogs; Cell Differentiation process; Cell Nucleus; Cells; Chromatin; Chromatin Structure; Chromosomal Rearrangement; Chromosomal translocation; Chromosome Fragile Sites; Chromosomes; Complex; DNA; DNA Double Strand Break; DNA Repair; DNA Sequence Rearrangement; DNA-Protein Interaction; Data; Data Set; Development; Disease; Frequencies; Future; Gene Expression; Gene Expression Regulation; Genes; Genome; Genome Stability; Genomics; Goals; Health; Human; Human Genome; Lead; Link; Location; Maintenance; Malignant Neoplasms; Measures; Mediating; Modeling; Molecular Conformation; Mus; Oncogenic; Organ; Physics; Polymers; Predisposing Factor; Predisposition; Probability; Property; Publishing; Radiation Induced DNA Damage; Recurrence; Regulatory Element; Research; Role; Stress; Structure; Techniques; Technology; Testing; Tissue Engineering; Tissues; anticancer research; base; cancer therapy; cell behavior; experience; human disease; human tissue; insight; meter; migration; physical model; physical property; repaired; research study; response; simulation; success; tool; tumor progression

DESCRIPTION (provided by applicant): The three-dimensional (3D) organization of the human genome in the nucleus is important not only for packing 2 meters of DNA inside a 2 micron diameter nucleus, but also for gene regulation and other important biological functions. Taking advantage of the Hi-C technology recently developed to capture chromosome folding and looping throughout the genome within a cell, the proposed research will investigate the relationship between this genome organization and physical disruptions experienced by the cell and DNA. The dramatic physical disruption of a DNA double strand break (DSB) can lead to cancer and other diseases if chromosomal translocations resulting from incorrect break repair disrupt genes or the relationship between genes and regulatory elements. Thus, it is important to understand the factors influencing which translocations are likely to occur after a DSB. Hi-C experiments measuring genome organization in mouse B lymphocytes will be used to determine the extent to which pre-existing proximity of genomic regions correlates with the locations of translocations observed after an induced DSB in the same cells. In cases where a high probability of physical proximity does not explain recurrent translocations, the contribution of other factors to translocation susceptibility will be examined by computationally integrating interaction and translocation data obtained in this research with previously published data on features such as gene expression, protein-DNA interactions, and chromosomal common fragile sites. The influence of the physical properties of the 3D genome structure on the formation of translocations between non-proximal genome regions will then be evaluated by comparing experimentally observed translocations with a biophysical model of the genome derived from principles of polymer physics and experimental Hi-C data. This model will be used to predict how much the physical properties of the genome structure might constrain or enhance the movability of genomic regions and broken ends of DNA in their search for repair partners. These simulations will be followed by direct experimental tests of the deformability of the genome by performing Hi-C experiments on cells subjected to physical forces and constraints. The results of these force experiments will test the biophysical model predictions and enable comparisons between physical deformability and translocation susceptibility. Successfully observing the response of the genome inside cells to physical forces will also provide insight into whether biologically relevant forces in tissues and organs might influence gene expression, cell behavior, and cell fate by direct changes to the chromatin structure. Such insight could contribute to future applications of force in the directed differentiation of cells for tissue engineering purposes. By integrating new experimental data, physical models, and previously published genomic data, this research will contribute to a more complete understanding of the factors involved in the response of the complex 3D genome to physical disruptions in health and disease. PUBLIC HEALTH RELEVANCE: This project investigates how the effects of physical disruptions to cells and DNA, which often affect human health, are related to the three dimensional organization of DNA within the cell nucleus. Understanding how genome organization affects chromosomal rearrangements that can occur after DNA breakage will help explain the origin and progression of cancers that are often caused or affected by these rearrangements. Measuring the effects of other forces and stresses felt by the cell on genome organization will provide information about how forces on cells in human tissues and organs can affect their proper development and function.

描述（由申请人提供）：人类基因组在细胞核中的三维（3D）组织不仅对于在直径2微米的细胞核内包装2米的DNA很重要，而且对于基因调控和其他重要的生物学功能也很重要。利用最近开发的Hi-C技术来捕获细胞内整个基因组中的染色体折叠和环，拟议的研究将调查这种基因组组织与细胞和DNA所经历的物理破坏之间的关系。如果不正确的断裂修复导致染色体易位破坏基因或基因与调控元件之间的关系，DNA双链断裂（DSB）的剧烈物理破坏可导致癌症和其他疾病。因此，了解影响DSB后可能发生易位的因素是很重要的。测量小鼠B淋巴细胞基因组组织的Hi-C实验将用于确定在相同细胞中诱导DSB后观察到的基因组区域先前存在的接近程度与易位位置的相关性。在物理接近的高概率不能解释易位复发的情况下，其他因素对易位易感性的贡献将通过计算整合本研究中获得的相互作用和易位数据，以及先前发表的基因表达、蛋白质- dna相互作用和染色体共同脆弱位点等特征的数据来检验。三维基因组结构的物理性质对非近端基因组区域间易位形成的影响将通过比较实验观察到的易位与基于聚合物物理原理和实验Hi-C数据的基因组生物物理模型来评估。该模型将用于预测基因组结构的物理特性在多大程度上限制或增强基因组区域和DNA断裂端在寻找修复伙伴时的可移动性。这些模拟之后，将通过对受物理力和约束的细胞进行Hi-C实验，对基因组的可变形性进行直接实验测试。这些力实验的结果将测试生物物理模型的预测，并使物理变形能力和易位敏感性之间的比较成为可能。成功地观察细胞内基因组对物理力的反应，也将有助于深入了解组织和器官中的生物学相关力是否可能通过直接改变染色质结构来影响基因表达、细胞行为和细胞命运。这样的洞察力可能对未来有所贡献