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症的表型是由于缺失基因本身的破坏而产生的。与这一教条形成直接对比的是，我们提出，遗传性疾病可以由物理上的、远程相互作用的变化引起或修改，这些相互作用通常发生在现在被删除的基因座和绘制在线性遗传图谱上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的相互作用不同，我们认为一个共同调控的基因网络在物理上是共定位的，表型差异是由于不同个体中这个染色质中心的不同辐条的组合破坏造成的。由于缺失综合征通常以多种表型为特征，我们将检验我们对最常见的基因组缺失障碍--人类22q11缺失(Del22q11)的假设，该疾病的特征是显著的表型变异。Del22q11可能是精神分裂症最常见的遗传危险因素。我们已经在8条染色体上确定了一个由13个基因组成的中枢，它与22q11物理上相互作用。我们将研究含有缺失的全表型患者的DNA和RNA样本，以及来自正常和受影响患者的细胞系。1)使用我们最近发表的发现长距离染色质相互作用的新方法--关联染色体陷阱分析，我们将识别所有与22q11常见缺失区域物理上相互作用的基因。2)我们将使用荧光原位杂交和高分辨率分子分析染色体构象捕捉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。4)我们将使用基因敲除小鼠来确认这个枢纽上的基因在心脏发育和疾病中的作用。这一提议是高风险的，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量致病基因。这一假说的影响将从遗传综合征延伸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。 与公共健康相关：不同染色体上的基因可能在物理上相互作用，并影响这些基因在细胞中的工作方式。在一些癌症和遗传性疾病中，基因之间的这些长距离联系会因为染色体的一部分被删除而丢失。通过研究基因之间的远程相互作用网络，我们将了解疾病是如何由许多基因表达的变化引起的，当这些基因失去相互作用时，这些基因变得异常调节。

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.