Role of Long-Range Chromatin Interactions in Genetic Disease

描述（由申请人提供）：医学遗传学的一个中心范式是缺失综合征的表型是由缺失基因本身的破坏引起的。与这一教条直接相反，我们提出遗传性疾病可以由物理上的变化引起或改变，这种变化通常发生在现在被删除的位点和在线性遗传图谱上绘制时远离被删除区域的基因之间。然而，与关注单个缺失候选基因相互作用相反，我们提出一个共调控基因网络在物理上共定位，并且表型变异是由不同个体中该染色质中心不同辐条的组合破坏引起的。由于缺失综合征通常以多种表型为特征，我们将在最常见的基因组缺失疾病——人类22q11缺失（del22q11）上验证我们的假设，其特征是显着的表型变异。Del22q11可能是精神分裂症最常见的遗传风险因素。我们已经确定了8条染色体上的13个基因中心与22q11物理相互作用。我们将研究含有缺失的完全表型患者的DNA和RNA样本，以及正常和受影响患者的细胞系。1)使用相关染色体诱捕法（Associated Chromosome Trap assay）——我们最近发表的用于发现远端染色质相互作用的新方法，我们将识别所有与22q11常见缺失区域物理相互作用的基因。2)我们将使用荧光原位杂交和高分辨率分子测定染色体构象捕获来证实这些相互作用发生在健康个体中。3)然后我们可以使用这个相关基因目录来检查它们在疾病表现中的潜在作用。我们将使用敲除小鼠来确认该中心的基因在心脏发育和疾病中的作用。这个建议是高风险的，因为我们的目标是关注物理网络本身，而不是组成这些网络的高产致病基因。这一假说的影响将从遗传综合征扩展到癌症中的染色体重排，它将揭示和解释复杂疾病的遗传风险。

DESCRIPTION (provided by applicant): A central paradigm of medical genetics is that the phenotype of a deletion syndrome results from the disruption of the deleted genes themselves. In direct contradistinction to this dogma, we propose that genetic diseases can be caused or modified by changes in physical, long-range interactions that normally occur between loci that are now deleted and genes that are far from the deleted region when plotted on a linear genetic map. In contrast to focusing on singe deletion-candidate gene interaction, though, we propose that a network of co- regulated genes physically co-localizes, and that phenotypic variation results from the combinatorial disruption of different spokes of this chromatin hub in different individuals. Since deletion syndromes are often characterized by multiple phenotypes, we will test our hypothesis on the most common genomic deletion disorder, deletion of human 22q11 (del22q11), which is characterized by remarkable phenotypic variation. del22q11 may be the most common genetic risk factor for schizophrenia. We have identified a hub of 13 genes on 8 chromosomes that physically interacts with 22q11. We will study DNA and RNA samples from fully phenotyped patients who harbor the deletion, as well as cell lines from normal and affected patients. 1) Using the Associated Chromosome Trap assay, our recently published novel methodology for discovering long-range chromatin interactions, we will identify all genes that physically interact with the commonly deleted region of 22q11. 2) We will confirm that these interactions occur in healthy individuals using fluorescent in situ hybridization and the high-resolution molecular assay chromosome conformation capture. 3) We can then use this catalog of associated genes to examine their potential roles in disease manifestation. 4) We will use knock-out mice to confirm the role of the genes in this hub in cardiac development and disease. This proposal is high-risk because we aim to focus on the physical network itself, rather than the high-yield disease-causing genes that compose those networks. The impact of this hypothesis will extend beyond genetic syndromes to chromosomal rearrangements in cancers, and it will uncover and explain genetic risks for complex diseases. PUBLIC HEALTH RELEVANCE: Genes on different chromosomes may physically interact with each other and affect the way those genes work in a cell. In some cancers and genetic diseases, these long range associations between genes are lost because a part of a chromosome becomes deleted. By examining the network of long range interactions among genes, we will learn how diseases are caused by the change in the expression of many genes which become abnormally regulated when the interactions are lost.