Dissecting the transciptional network governing differentiation of periderm

描述(申请人提供)：浅表上皮(如口腔上皮、表皮)的异常分化是结构性出生缺陷的共同病因，从口腔裂伤到先天性鱼鳞病。连锁和关联研究证实，这些遗传性疾病有遗传基础。然而，在口面部裂的情况下，只有大约一半的可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，迫切需要确定控制表面上皮细胞发育的调节分子，并确定它们之间的相互作用。如果不彻底了解负责浅层上皮细胞发育的整个基因调控网络，希望预测这些疾病风险的遗传顾问的努力将继续受到严重限制。斑马鱼胚胎皮肤或周皮是一种易于处理的表层上皮模型。在这里，我们提出了一种体内系统生物学的方法来推断控制斑马鱼周皮分化的转录网络的结构。在目标1中，我们将通过广泛的体内扰动分析来做到这一点，包括上位性实验。此外，在目标2中，通过使用体内报告研究和计算分析的组合方法，我们将识别控制周皮表达的顺式调控模块。我们将测试这样一种假设，即在网络层次结构中同一级别活动的增强器将共享一个共同的组织。我们的团队包括一名在斑马鱼胚胎学方面具有专业知识的研究员和一名在模型系统中顺式调控模块的基因组分析方面具有专业知识的研究人员。这项拟议工作的成功完成将是迄今为止对推动脊椎动物细胞类型分化的反式和顺式作用元件进行的最详尽的分析。因此，我们预期的结果是在理解表面上皮细胞的发育方面取得显著进展，从而提高识别编码和调控DNA中的序列多态的能力，这些DNA序列多态是上皮分化疾病的病原体，包括皮肤和口面部裂隙疾病。

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.