A Center for Zebrafish Chromatin and Epigenetics

描述（由申请人提供）：我们将创建一个资源，用于研究早期斑马鱼发育中的染色质结构，表观遗传修饰和转录调节因子。该资源将被命名为捷克，斑马鱼表观遗传学和染色质中心。染色质调节基因表达，并通过影响驱动细胞生长和命运决定的转录程序来影响发育。DNA甲基化和其他染色质标记（定义为表观基因组）强烈影响发育过程中特定基因表达的时间和强度，但尚未在任何生物体中进行系统研究。此外，通过染色质的转录错误调控是许多发育缺陷和某些癌症的基础。因此，我们必须了解染色质动力学如何帮助指导发育。该中心将结合使用基因组和遗传方法来解决这个问题，将为基因组方法提供详细的协议，并将部署和管理一个数据库，供社区查看和提交数据集。在这里，我们将定义生殖细胞和斑马鱼的早期胚胎的基本表观基因组，在器官规格之前和期间。我们将结合染色质免疫沉淀（ChIP）与高密度基因组平铺阵列（检查染色质），并进行基因表达谱分析。我们将首先将我们的研究限制在与转录抑制（DNA甲基化，H3K9me3和H3K27me3）或转录激活（H3K4me3）最密切相关的染色质修饰上，其中包括对干细胞中定位基因重要的“二价”修饰。值得注意的是，我们的初步研究表明，精子染色质的早期发育调节因子是通过DNA低甲基化来调节的。在后期胚胎中，我们将使用FACS分离发育组织，然后确定其表观基因组。

DESCRIPTION (provided by applicant): We will create a resource for the investigation of chromatin structure, epigenetic modifications, and transcriptional regulators in early zebrafish development. The resource will be named CZECH, the Center for Zebrafish Epigenetics and CHromatin. Chromatin regulates gene expression, and impacts development by influencing the transcriptional programs that drive cell growth and fate decisions. DNA methylation and other chromatin marks (defined as the epigenome) strongly influence the timing and strength of expression of particular genes during development, but a systematic study has not been performed in any organism. Furthermore, misregulation of transcription via chromatin underlies many developmental defects and certain cancers. Thus, we must understand how chromatin dynamics help guide development. The Center will address this issue using a combination of genomic and genetic approaches, will provide detailed protocols for genomic approaches, and will deploy and manage a database for the community to view and submit datasets. Here, we will define the basic epigenome of germ cells and the early embryo of the zebrafish, both before and during organ specification. We will combine chromatin immunoprecipitation (ChIP) with high-density genome tiling arrays (to examine chromatin), and also perform gene expression profiling. We will initially limit our examination to the chromatin modifications most closely associated with transcriptional repression (DNA methylation, H3K9me3, and H3K27me3), or transcriptional activation (H3K4me3), which include the `bivalent' modifications important for poising genes in stem cells. Notably, our preliminary studies suggest the poising of early developmental regulators in sperm chromatin by DNA hypomethylation. In later stage embryos, we will use FACS to isolate developing tissues and then determine their epigenome. PUBLIC HEALTH RELEVANCE: This project addresses how chromosomes and their resident genes are packaged in germ cells and then change their packaging following fertilization to regulate gene expression during early development. This process is central to understanding how cells differentiate, how organs develop, and how cell growth is regulated. The misregulation of chromosome and gene packaging leads to problems such as birth defects, retardation, or cancer, depending on the particular chromosome(s) or gene(s) affected.