Identifying the Atoh1 targetome in hair cells with deep sequencing

通过深度测序鉴定毛细胞中的 Atoh1 靶标组

基本信息

批准号：
8366669
负责人：
Andrew K Groves
金额：
$ 23.48万
依托单位：
BAYLOR COLLEGE OF MEDICINE
依托单位国家：
美国
项目类别：
财政年份：
2012
资助国家：
美国
起止时间：
2012-07-20 至 2014-06-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8366669
关键词：
Address Adult Age Animals Antibodies Auditory Binding Binding Sites Bioinformatics Boxing Candidate Disease Gene Cell Differentiation process Cell physiology Cells Cellular Structures Cerebellum Cessation of life ChIP-seq Chromatin Cochlea Collaborations Complex Coupled DNA DNA Binding Data Set Development Distal Ear Ectopic Expression Environmental Risk Factor Equilibrium Exploratory/Developmental Grant Failure Gene Targeting Generic Drugs Genes Genetic Genomics Goals Hair Cells Hearing problem Histone H3 Histones In Vitro Individual Inherited Knock-in Mouse Labyrinth Lysine Mammals Mediating Medicine Methods Mono-S Mus Mutant Strains Mice Natural regeneration Newborn Infant Noise Nucleic Acid Regulatory Sequences Organ Pharmaceutical Preparations Pilot Projects Play Property Proteins Publishing RNA Sequences Regulator Genes Retirement Role Sensory Sensory Hair Site System Systems Biology Techniques Technology Time United States Vertebrates Vestibular Hair Cells Work age related antineoplastic antibiotics chromatin immunoprecipitation college design disability equilibration disorder gene therapy genome-wide analysis granule cell hair cell regeneration hearing impairment high risk in vivo interest killings next generation promoter regenerative therapy research study response sound technology development therapy design tool transcription factor

项目摘要

DESCRIPTION (provided by applicant): Hearing and balance disorders are some of the most common disabilities in the United States, with 0.1% of newborns having some form of hereditary hearing loss and roughly half of all adults suffering from some degree of hearing loss by the time they reach retirement age. The causes of age-dependent hearing loss are complex, with both genetic and environmental factors playing a role. The most common reason for hearing loss is the death of sensory hair cells in the inner ear. In addition to genetic factors, damage from noise exposure or from certain kinds of antibiotics and chemotherapy drugs can kill hair cells. Once hair cells die in mammals, they are never replaced and hearing loss is therefore permanent. Many experiments over the last 15 years have suggested that the transcription factor Atoh1 plays a central role in the development of sensory hair cells. First, it is one of the earliest genes to be expressed in differentiating hair cells. Second, inactivation of Atoh1 in mice causes a complete failure of hair cell differentiation in both the cochlear and vestibular sensory organs. Third, Atoh1 is one of the first genes to be expressed during hair cell regeneration in non-mammalian vertebrates. Finally, ectopic expression of Atoh1 is sufficient to generate new hair cells in some regions of the inner ear in vitro and in vivo. For these reasons, Atoh1 has been proposed as tool for gene therapy to replace lost auditory or vestibular hair cells. Despite the great interest in Atoh1's function in development and its potential use in regenerative therapies, very little is known about the genes that are regulated by Atoh1 in hair cells. At one extreme, Atoh1 might regulate a relatively small number of other transcription factors, which would each regulate different aspects of hair cell development, maturation and survival. Alternatively, Atoh1 might have a much broader role in directly regulating many aspects of hair cell structure and function. Moreover, it is not clear whether Atoh1 transcriptional targets differ between auditory and vestibular hair cells, or whether these differences are determined by other factors, with Atoh1 simply regulating generic hair cell properties. In this pilot project, we propoe to use cutting-edge deep sequencing and bioinformatic approaches to identify the direct targets of Atoh1 in hair cells - the so-called Atoh1 "targetome". We will work in collaboration with Dr. Huda Zoghbi at Baylor College of Medicine, whose lab recently used similar technology to successfully characterize the Atoh1 targetome in cerebellar granule cells. A gene that is directly regulated by Atoh1 should possess three attributes - it should be expressed in an Atoh1-dependent manner, the genomic locus of the gene should be transcriptionally active, and Atoh1 protein should bind to regulatory regions adjacent to the gene. The successful strategy of the Zoghbi lab involved a genome-wide analysis of these three properties, coupled with statistical ranking to generate a list of direct Atoh1 targets. We now propose to apply these same methods to identify the Atoh1 targetome in hair cells. PUBLIC HEALTH RELEVANCE: Sensory hair cells are specialized cells in the inner ear that detect sound and mediate our sense of balance. This project will identify genes that are important for the development and survival of sensory hair cells. The long term goal is to use this information to design therapies for individuals who suffer hearing or balance disorders due to the loss of sensory hair cells.

描述（由申请人提供）：听力和平衡障碍是美国一些最常见的残疾，有0.1％的新生儿具有某种形式的遗传性听力损失，并且在达到退休年龄时患有某种程度的听力损失的所有成年人中，大约有一半。依赖年龄的听力损失的原因很复杂，遗传因素和环境因素都起作用。听力丧失的最常见原因是内耳感官毛细胞的死亡。除了遗传因素外，噪声暴露或某些类型的抗生素和化学疗法药物的损害还可以杀死毛细胞。一旦毛细胞死于哺乳动物，它们就永远不会被替换，因此听力损失将是永久的。在过去15年中，许多实验表明，转录因子ATOH1在感觉毛细胞的发展中起着核心作用。首先，它是最早的基因在区分毛细胞中表达。其次，小鼠AtoH1失活在人工耳蜗和前庭感觉器官中导致毛细胞分化的完全失败。第三，ATOH1是非哺乳动物脊椎动物中毛细胞再生期间最早表达的基因之一。最后，ATOH1的异位表达足以在体外和体内产生新的毛细胞。由于这些原因，已提出ATOH1作为基因疗法的工具，以替代失去的听觉或前庭毛细胞。尽管对ATOH1在发育中的功能及其在再生疗法中的潜在用途非常感兴趣，但对毛细胞中ATOH1调节的基因知之甚少。在一个极端情况下，ATOH1可能调节相对较少的其他转录因子，这些因素将调节毛细胞发育，成熟和存活的不同方面。另外，ATOH1在直接调节毛细胞结构和功能的许多方面可能具有更广泛的作用。此外，尚不清楚ATOH1转录目标是否有所不同在听觉和前庭毛细胞之间，或者这些差异是否由其他因素决定，而ATOH1只是调节通用毛细胞的性质。在这个试点项目中，我们提出使用最先进的深度测序和生物信息学方法来识别毛细胞中ATOH1的直接靶标 - 所谓的ATOH1“ Targetome”。我们将与贝勒医学院的Huda Zoghbi博士合作，他的实验室最近使用类似的技术成功地描述了小脑颗粒细胞中的AtoH1 Targetome。由ATOH1直接调节的基因应具有三个属性 - 应以ATOH1依赖性方式表达，该基因的基因组基因座应具有转录活性，ATOH1蛋白应与邻近基因的调节区域结合。 Zoghbi实验室的成功策略涉及对这三个特性的全基因组分析，并加上统计排名，以生成直接ATOH1目标列表。现在，我们建议采用这些相同的方法来识别毛细胞中的ATOH1靶体。公共卫生相关性：感觉毛细胞是内耳中的专门细胞，可检测声音并介导我们的平衡感。该项目将确定对感觉毛细胞的发育和存活至关重要的基因。长期目标是使用这些信息来设计因感觉毛细胞损失而遭受听力或平衡疾病的人的疗法。