Dissecting the transciptional network governing differentiation of periderm

描述（由申请人提供）：表面上皮（如口腔上皮、表皮）的异常分化是结构性出生缺陷（从口面裂到先天性鱼鳞病）的共同病因。连锁和关联研究证实，这些遗传疾病具有遗传基础。然而，在唇腭裂的情况下，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，编码蛋白如何促进表皮分化仍然知之甚少。因此，仍然迫切需要确定控制浅表上皮发育的调节分子，并确定它们之间的相互作用。如果没有对负责表皮上皮发育的整体基因调控网络的透彻理解，遗传咨询师希望预测这些疾病风险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浅表上皮模型。在这里，我们提出了一种体内的系统生物学方法来推断斑马鱼周皮分化的转录网络的结构。我们将这样做，在目标1中，通过广泛的体内扰动分析，包括上位实验。此外，在目标2中，通过使用体内报告研究和计算分析的结合方法，我们将确定控制周周表达的顺式调控模块。我们将测试一个假设，即在网络层次结构的同一级别上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具有斑马鱼胚胎学专业知识的研究员和一名具有模型系统中顺式调节模块基因组分析专业知识的研究员。这项工作的成功完成将构成迄今为止对驱动任何脊椎动物细胞类型分化的反式和顺式作用元件的最详尽的分析。因此，我们的预期结果是在理解浅表上皮的发育方面取得巨大进展，从而提高识别编码和调控DNA序列多态性的能力，这些序列多态性是上皮分化疾病的病原，包括皮肤疾病和口腔-面部裂。

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.