Genome-wide analysis of DNA methylation and its regulation by hormones during post-embryonic brain development

该项目的目标是通过研究甲状腺激素（TH）在早期发育基因表达调节中的新作用来促进对大脑发育的了解。 众所周知，基因的表达部分是由脱氧核糖核酸（DNA）和DNA周围蛋白质的化学修饰控制的。这些所谓的“表观遗传修饰”导致基因功能的可遗传变化，而不涉及DNA序列本身的变化。最近的研究结果表明，表观遗传修饰在生物体发育，生理和行为中起着关键作用，并与从癌症到复杂行为障碍（如自闭症和精神分裂症）的人类疾病有关。一种这样的表观遗传修饰是向DNA中的胞嘧啶残基添加甲基（DNA甲基化）。基因调控区的可变DNA甲基化可以影响基因表达。DNA甲基化通常促进基因抑制，而DNA去甲基化促进基因激活。然而，发育过程中大脑中DNA甲基化的模式和功能以及控制DNA甲基化的因素知之甚少。首席研究员（PI）最近发现，TH，这是已知的中枢神经系统的正常发育至关重要，控制DNA甲基化在发育中的大脑。在这里，他将使用青蛙作为模型系统来研究TH的DNA甲基化机制及其对神经发育的影响。该项目还将涉及培训多样化的科学工作队伍，为生命科学家开设实验设计本科课程，以及与中学生和退休社区的成年人开展科学宣传活动。该项目的具体目标是：1）使用全基因组分析，包括RNA测序、染色质免疫沉淀测序和甲基捕获测序，绘制发育中的脑中的DNA甲基化模式，2）使用TH依赖性酶向染色质的募集的靶向分析，确定TH调节DNA甲基化的机制，3）通过分析细胞周期调控了解TH调控DNA甲基化对神经发育的影响。 PI将专注于青蛙非洲爪蟾（Silurana）热带的变态，一个很好的研究TH依赖的过程。他们将进行全基因组甲基化和转录因子关联分析，以研究DNA甲基化在胚后大脑发育过程中的模式和作用。拟议研究的结果将提供对调节神经细胞表观遗传景观的因素的更深入了解，并将为研究DNA甲基化在神经发育和功能中的调控和作用开辟新途径。

The goal of this project is to advance understanding of brain development by studying a novel role of thyroid hormone (TH) in the regulation of gene expression in early development. It is known that the expression of genes is controlled in part by chemical modifications to deoxyribonucleic acid (DNA) and the proteins that surround the DNA. These so-called 'epigenetic modifications' result in heritable changes in gene function that do not involve changes to the DNA sequence itself. Recent findings show that epigenetic modifications play pivotal roles in organismal development, physiology, and behavior, and are implicated in human diseases from cancer to complex behavioral disorders, such as autism and schizophrenia. One such epigenetic modification is the addition of methyl groups to cytosine residues in DNA (DNA methylation). Variable DNA methylation at gene regulatory regions can influence gene expression. DNA methylation typically promotes gene repression, whereas DNA demethylation promotes gene activation. However, the patterns and functions of DNA methylation in the brain during development, and the factors that control DNA methylation are poorly understood. The Principal Investigator (PI) recently discovered that TH, which is known to be critical for normal development of the central nervous system, controls DNA methylation in the developing brain. Here, he will examine the mechanism of DNA methylation by TH and its consequences for neurological development using the frog as model system. The project also will involve training of a diverse scientific workforce, establishment of an undergraduate course in experimental design for life scientists, and science outreach activities with middle school students and with adults at retirement communities. The specific aims of this project are to: 1) map DNA methylation patterns in the developing brain using genome-wide analyses including RNA sequencing, chromatin immunoprecipitation sequencing, and methyl capture sequencing, 2) determine the mechanisms by which TH regulates DNA methylation using targeted analysis of TH-dependent recruitment of enzymes to chromatin, and 3) understand the consequences of TH regulation of DNA methylation for neurological development through analysis of cell cycle control. The PI will focus on metamorphosis of the frog Xenopus (Silurana) tropicalis, a well studied TH-dependent process. They will conduct genome-wide methylation and transcription factor association analyses to investigate the patterns and roles of DNA methylation during postembryonic brain development. The results of the proposed research will provide a deeper understanding of factors that modulate the epigenetic landscape in neural cells, and will open new avenues for research on the regulation and roles of DNA methylation in neurological development and function.