In toto imaging and genomics to decode ear hair cell formation and regeneration

描述（由申请人提供）：听力和平衡丧失是人类普遍存在的一种使人衰弱的疾病，主要是由内耳主要感觉细胞毛细胞的丧失引起的。人类的毛细胞不会自然再生，而斑马鱼等动物的毛细胞则很容易再生。为了了解毛细胞在发育过程中的形成和毛细胞再生对损伤的反应，我们将采用基于综合系统生物学的方法。我们的方法集成了toto成像，提供了系统的高分辨率分析，跨越空间和时间的毛细胞生成和组学方法，允许系统分析整个基因组的转录活性。具体来说，我们将使用toto成像技术，一项我们开发的技术，来生成一个四维的，基于细胞的数字耳，全面量化斑马鱼毛细胞形成和再生的细胞过程。我们将使用细胞类型特异性组蛋白修饰的ChIP-seq来确定在毛细胞生成的所有关键步骤中，整个基因组中活跃的增强子、启动子和绝缘子。生物信息学方法将被用于在定义的增强子内绘制转录因子结合位点到它们控制的基因，从而在我们的数字耳朵的虚拟细胞内构建一个全面的顺式调控网络。这项研究将为基因组如何编码毛细胞的逐步规范提供前所未有的见解，对人类毛细胞再生具有潜在的重要意义。听力和平衡方面的缺陷很普遍，而且使人衰弱。它们主要是由内耳毛的感觉细胞（毛细胞）的丧失引起的，这种细胞在人类身上不能再生，但在其他动物身上可以。我们试图了解内耳毛细胞再生的遗传和细胞控制。

DESCRIPTION (provided by applicant): Loss of hearing and balance is a widespread and debilitating medical condition in humans, and is predominantly caused by a loss of hair cells, the primary sensory cell of the inner ear. Hair cells do not naturally regenerate in humans, in contrast to other animals such as zebrafish where hair cells readily regenerate. To understand hair cell formation during development and hair cell regeneration in response to damage we will undertake an integrative systems biology based approach. Our approach integrates in toto imaging which provides systematic high resolution analysis across the space and time of hair cell generation with omic approaches that allow systematic analysis of transcriptional activity across the genome. Specifically, we will use in toto imaging, a technology we developed, to generate a 4-dimensional, cell-based Digital Ear that comprehensively quantifies the cellular processes that form and regenerate hair cells in zebrafish. We will use cell-type-specific ChIP-seq of histone modifications to determine the enhancers, promoters, and insulators active across the entire genome at all the key steps of hair cell generation. Bioinformatic approaches will be used to map transcription factor binding sites within defined enhancers to the genes they control to construct a comprehensive cis-regulatory network within the virtual cells of our Digital Ear. This research will provide unprecedented insight into how the genome encodes the stepwise specification of hair cells, with potentially important implications for hair cell regeneration in humans. Relevance to Health Deficiencies in hearing and balance are widespread and debilitating. They are principally caused by loss of the sensory cells (hair cells) of the inner ear hair which cannot regenerate in humans but can in other animals. We seek to understand the genetic and cellular control of inner ear hair cell regeneration. PUBLIC HEALTH RELEVANCE: Deficiencies in hearing and balance are widespread and debilitating. They are principally caused by loss of the sensory cells (hair cells) of the inner ear hair which cannot regenerate in humans but can in other animals. We seek to understand the genetic and cellular control of inner ear hair cell regeneration.