Species-specific chromatin structure and its environmental interaction in craniofacial skeletal development andvariation using cichlid fishes

项目摘要 颅面骨骼的变异产生了一系列独特的面孔， 畸形先天性颅面畸形是最常见的出生缺陷之一。除了 随着遗传变化的不断增加，我们越来越认识到DNA的物理包装在遗传过程中的重要性。 基因表达和发育的调控，以及由此产生的基因型-表型关系。一个主要 这种表观遗传调控的决定因素是组蛋白的翻译后修饰， 染色质的结构和DNA的获取。这项工作的目标是确定染色质的变化是如何 结构，特别是组蛋白乙酰化，影响面部骨骼的表型变化。我们将利用 在非模式慈鲷鱼的进化辐射之间的无与伦比的自然颅面变化。 鉴于慈鲷科鱼类面部变异模仿人类面部变异， 在脊椎动物中是保守的，这可能会对人类变异的表观遗传基础产生新的见解。 脸上在目标1中，我们将全面量化染色质结构和DNA可及性的变化， ATAC-seq（转座酶可降解染色质的测定）和下游转录效应， RNA测序这些基因组分析将在三种具有不同成年形态的慈鲷中进行 在面部分化的三个关键发育时间点在目标2中，我们将使用药理学试剂， 在面部发育的不同窗口期间改变与组蛋白乙酰化相关的蛋白质的活性。 我们将重点关注四种药物，它们是人类出生缺陷的潜在来源;这些药物正在临床上 用于治疗从癌症到心脏病的疾病的试验，但FDA目前没有注意到潜在的 孕妇的风险。这一目标的完成将确定表观遗传变化的敏感性窗口 和潜在的致畸作用。将这些药物应用于密切相关的慈鲷（相当于 比较不同的小鼠品系），允许研究基因与环境（GxE）的相互作用， 类似的药物。这项工作将解决我们对基因型知识的一个主要空白- 表型关系，表观遗传调控在表型变异中的作用。药物在丽鱼中的应用 鱼类能够发现遗传相互作用，可以定义暴露的敏感性和颅面神经损伤的风险。 人类的畸形根据R15区域补助金的目标，本科生将进行 目标1中的生物信息学分析，目标2中的先导药理学操作。基金将支持 四名新的本科生研究人员，包括夏季奖学金，使他们能够完全沉浸在研究中 没有课程表的限制。

PROJECT SUMMARY Variation in the craniofacial skeleton produces both a spectrum of unique faces and as well as clinical malformations. Congenital craniofacial anomalies are one of the most common birth defects. In addition to genetic changes, we are increasingly recognizing the importance of the physical packaging of DNA in the regulation of gene expression and development, and the resulting genotype-phenotype relationship. A major determinant of this epigenetic regulation is post-translational modifications of histone proteins, which alters the structure of chromatin and access to DNA. The goal of this work is to determine how variation in chromatin structure, in particular histone acetylation, impacts phenotypic variation of the facial skeleton. We will capitalize on the unparalleled natural craniofacial variation among the evolutionary radiation of non-model cichlid fishes. Given that cichlid facial variation mimics human facial variation and the molecular control of facial development is conserved across vertebrates, this may yield novel insights into the epigenetic basis of variation in human faces. In Aim 1, we will comprehensively quantify variation in chromatin structure and DNA accessibility using ATAC-seq (Assay for Transposase Accessible Chromatin) and the downstream transcriptional effects using RNA-seq. These genomic analyses will be conducted in three cichlid species with diverse adult morphologies at three developmental time points key for facial divergence. In Aim 2, we will use pharmacological agents to alter the activity of proteins associated with histone acetylation during distinct windows of facial development. We will focus on four drugs that are potential sources of birth defects in humans; these drugs are in clinical trials for treatment of diseases from cancer to heart disease, but the FDA does not currently note a potential risk for pregnant women. Completion of this aim will determine windows of sensitivity for epigenetic changes and potential teratogenic effects of these drugs. Applying these drugs in closely-related cichlids (comparable to comparing different mouse strains), allows investigation of gene by environment (GxE) interactions previously demonstrated for similar drugs. This work will address a major gap in our knowledge of the genotype- phenotype relationship, the role of epigenetic regulation in phenotypic variation. Application of drugs to cichlid fishes enables discovery of genetic interactions that may define sensitivity to exposure and risk of craniofacial malformations in humans. In line with the goals of the R15 AREA grant, undergraduates will conduct bioinformatic analyses in Aim 1, and lead pharmacological manipulations in Aim 2. Grant funds will support four new undergraduate researchers, including summer fellowships that enable a full immersion in research without the constraints of a full class schedule.