Integrated multi-omics analyses of early mammalian craniofacial development

摘要 颅面畸形是世界范围内最常见的人类出生缺陷， 每年有多达20万名新生儿患有某种类型的颅面缺陷。这些缺陷可以 作为涉及多个组织和器官的复杂综合征的一部分发生。的综合征形式 这些疾病已经成功地与包括TWIST 1在内的近500个基因相关联， 颅缝早闭和IRF 6用于口面裂。然而，更常见的是，身体的其他部位都不 直接受累（50%颅缝早闭，70%口面裂）。全基因组关联研究 表明这种缺陷的遗传性，但绝大多数协会落在基因之外 这表明有缺陷的基因调控是这种缺陷发生的主要原因。基因 调节元件可以位于整个基因组中并且通常具有组织特异性活性， 这使得它们很难识别和预测它们控制的基因。本报告的总体目标 应用是整合早期人类和小鼠的表观基因组和转录组数据集 我们的实验室和FaceBase的颅面发育， 元素-基因相互作用我们的假设是， 人和小鼠富集了疾病相关生物学。在目标1中，我们建议 系统地鉴定了人类妊娠4.5 - 8周和小鼠妊娠4.5 - 8周的染色质状态， 胚龄9.5 - 15.5天。在目标2中，我们提出鉴定在细胞中协同调控的基因， 这两个物种在这些发展窗口。最后，在目标3中，我们建议将这两个 不同的网络类型来识别调控元件-基因配对。我们将通过实验验证 使用邻近结扎偶联的颅神经嵴细胞培养模型中的预测相互作用 免疫沉淀法。我们提出的研究将产生最全面的表观基因组 和转录组网络，并首次确定了保守的 构建哺乳动物口面复合体的调控结构。

Abstract Craniofacial abnormalities are some of the most commonly occurring human birth defects worldwide, with up to 200,000 children born every year with some type of craniofacial defect. These defects can occur as part of complex syndromes that involve multiple tissues and organs. The syndromic forms of these disorders have been successfully linked to nearly 500 genes including TWIST1 for craniosynostosis and IRF6 for orofacial clefting. However more frequently no other part of the body is directly involved (50% of craniosynostoses, 70% of orofacial clefts). Genome wide association studies indicate heritability for such defects, however the vast majority of associations fall outside of genes suggesting defective gene regulation is a major contributor to incidence of such defects. Gene regulatory elements can be located throughout the genome and typically have tissue-specific activity, making them difficult to identify and predict what gene they control. The overall objective of this application is to integrate epigenomic and transcriptomic data sets from early human and mouse craniofacial development from our lab as well as FaceBase to comprehensively predict regulatory element-gene interactions. Our hypothesis posits that conserved regulatory networks between human and mouse are enriched for disease relevant biology. In Aim 1 we propose to systematically identify chromatin states in human from 4.5 to 8 weeks of gestation and in mouse from embryonic days 9.5 to 15.5. In Aim 2 we propose to identify genes that are coordinately regulated in both species across these developmental windows. Finally, in Aim 3 we propose to integrate these two disparate network types to identify regulatory element-gene pairings. We will experimentally validate predicted interactions in a culture model of cranial neural crest cells using proximity-ligation coupled with immunoprecipitation. Our proposed studies will generate the most comprehensive epigenomic and transcriptomic networks in a developing human tissue and for the first time identify the conserved regulatory architecture for building the mammalian orofacial complex.