Integrated multi-omics analyses of early mammalian craniofacial development

摘要 颅面畸形是世界上最常见的人类出生缺陷之一， 每年有多达20万名儿童出生时患有某种类型的头面部缺陷。这些缺陷可能 作为涉及多个组织和器官的复杂综合征的一部分而发生。血液病的证候形式 这些疾病已经成功地与包括Twist1在内的近500个基因联系在一起 颅缝融合和IRF6治疗口面部裂。然而，更常见的是，身体的其他部位都不是 直接受累(50%的颅缝畸形，70%的口面部裂隙)。全基因组关联研究 表明这种缺陷的遗传性，然而，绝大多数关联属于基因之外 这表明基因调控缺陷是此类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， 这使得他们很难识别和预测他们控制的基因。这样做的总体目标是 应用是整合早期人类和小鼠的表观基因组和转录数据集 来自我们实验室和FaceBase的头面部发育综合预测调节 元素与基因的相互作用。我们的假说假设保守的监管网络在 人类和小鼠都丰富了与疾病相关的生物学。在目标1中，我们建议 系统鉴定妊娠4.5-8周的人和小鼠的染色质状态 胚胎天数为9.5至15.5天。在目标2中，我们建议识别在 这两个物种都跨越了这些发育窗口。最后，在目标3中，我们建议将这两者结合起来 识别调控元件-基因配对的不同网络类型。我们将通过实验验证 用邻近-结扎耦合的方法预测颅神经脊细胞培养模型中的相互作用 免疫沉淀法。我们提议的研究将产生最全面的表观基因组学 和转录网络在发育中的人类组织中，并首次识别保守的 用于构建哺乳动物口面部复合体的监管架构。

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.