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。与这一教条直接不同的是，我们提出，遗传疾病可以由物理上的变化引起或改变，当绘制在线性遗传图谱上时，通常发生在现在缺失的基因座和远离缺失区域的基因之间的长距离相互作用。然而，与关注单个缺失-候选基因相互作用相反，我们提出共调控基因的网络物理共定位，并且表型变异是由不同个体中该染色质枢纽的不同辐条的组合破坏引起的。由于缺失综合征的特点往往是多种表型，我们将测试我们的假设上最常见的基因组缺失疾病，人类22 q11（del 22 q11），其特点是显着的表型变异。del 22 q11可能是精神分裂症最常见的遗传危险因子。我们已经确定了8条染色体上的13个基因的中心，它们与22 q11发生物理相互作用。我们将研究来自携带缺失的完全表型患者的DNA和RNA样本，以及来自正常和受影响患者的细胞系。1)使用相关的染色体陷阱检测，我们最近发表的新方法，发现长距离染色质相互作用，我们将确定所有的基因，物理上与22 q11的常见缺失区域相互作用。2)我们将使用荧光原位杂交和高分辨率分子检测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的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证实该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，并将揭示和解释复杂疾病的遗传风险。 公共卫生相关性：不同染色体上的基因可能会相互作用，并影响这些基因在细胞中的工作方式。在某些癌症和遗传性疾病中，基因之间的这些长距离关联由于染色体的一部分被删除而丢失。通过研究基因之间的长程相互作用网络，我们将了解疾病是如何由许多基因表达的变化引起的，当相互作用丧失时，这些基因的表达变得异常调节。

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.