Dissecting the transciptional network governing differentiation of periderm

描述（由申请方提供）：浅表上皮（例如口腔上皮、表皮）的异常分化是从口面裂到先天性鱼鳞病等结构性出生缺陷的共同病因。连锁和关联研究证实，这些遗传疾病有遗传基础。然而，在口面裂的情况下，只有大约一半的遗传风险被分配给特定的基因。此外，即使在鱼鳞病的情况下，大多数常见形式的致病基因已经被发现，编码的蛋白质如何有助于表皮的分化仍然知之甚少。因此，仍然迫切需要鉴定控制浅表上皮细胞发育的调控分子，并确定它们之间的相互作用。如果不彻底了解负责浅表上皮细胞发育的整体基因调控网络，希望预测这些疾病风险的遗传咨询师的努力将继续受到严重限制。斑马鱼胚胎皮肤或骨膜是一种易于处理的浅表上皮细胞模型。在这里，我们提出了一个在体内，系统生物学的方法来推导的结构的转录网络管理分化的斑马鱼peridendum。我们将这样做，在目标1，通过广泛的体内扰动分析，包括上位性实验。此外，在目标2中，使用体内报告基因研究和计算分析的组合方法，我们将鉴定控制周膜表达的顺式调节模块。我们将测试的假设，在网络层次结构中的同一级别活跃的增强子将共享一个共同的组织。我们的团队包括一名具有斑马鱼胚胎学专业知识的研究人员和一名具有模型系统中顺式调控模块基因组分析专业知识的研究人员。成功完成所提出的工作将构成迄今为止进行的任何脊椎动物细胞类型的驱动分化的反式和顺式作用元件的最详尽的分析。因此，我们预期的结果是在理解浅表上皮细胞的发育方面取得了巨大的进展，从而提高了识别编码和调节DNA中序列多态性的能力，这些序列多态性是上皮分化疾病的致病因素，包括皮肤和口面裂缝疾病。

DESCRIPTION (provided by applicant): Abnormal differentiation of superficial epithelia (e.g. the oral epithelium, epidermis) is an etiology shared among structural birth defects ranging from orofacial clefting to congenital ichthyosis. Linkage and association studies confirm that these genetic disorders have a genetic basis. However, in the case of orofacial clefting only about half of the heritable risk has been assigned to specific genes. Moreover, even in the case of ichthyosis, for which the causative genes of most of the common forms have been discovered, how the encoded proteins contribute to the differentiation of epidermis remains only poorly understood. Thus there remains a critical need to identify regulatory molecules that control the development of superficial epithelia, and to determine the interactions among them. Without a thorough understanding of the overall gene regulatory network responsible for the development of superficial epithelia, the efforts of genetic counselors wishing to predict risk for these disorders will continue to be severely limited. The zebrafish embryonic skin or periderm is a tractable model for superficial epithelia. Here we propose an in vivo, systems biology approach to deduce the architecture of the transcriptional network governing differentiation of zebrafish periderm. We will do so, in Aim 1, through extensive in vivo perturbation analyses, including epistasis experiments. Further, in Aim 2, with a combined approach using in vivo reporter studies and computational analyses we will identify cis-regulatory modules that control expression in the periderm. We will test the hypothesis that enhancers that are active at the same level within the network hierarchy will share a common organization. Our team includes an investigator with expertise in zebrafish embryology and one with expertise in genomic analysis of cis-regulatory modules in model systems. Successful completion of the proposed work will constitute the most exhaustive analysis of trans- and cis- acting elements driving differentiation of any vertebrate cell type conducted to date. Our expected outcome therefore is a dramatic advance in understanding the development of superficial epithelia, resulting in an improved ability to recognize sequence polymorphisms in coding and regulatory DNA and that are pathogenic for diseases of epithelial differentiation, which include disorders of skin and oro-facial clefting.