Production sequencing of reference human epigenomes

描述（由申请人提供）：参考表观基因组制图中心（REMC）旨在通过ES细胞、分化细胞和组织的综合参考表观基因组的制作和综合分析，改变我们对人类表观遗传学的理解。为了实现这一目标，我们组建了一支独特的科学团队和基础设施，在干细胞生物学、表观基因组学、技术、生产研究和计算方面拥有广泛的专业知识和能力。我们最近展示了两种互补的方法，利用超高通量测序进行表观基因组分析。在第一种方法中，通过深度测序染色质IP DNA （ChlP-Seq）获得全基因组染色质图谱。第二种方法是通过高通量亚硫酸盐测序（HTBS）生成核苷酸分辨率的DNA甲基化图谱。这些方法代表了对先前工具的重大改进，因为它们产生精确的数字信息，具有高基因组覆盖率，需要更少的细胞并且具有成本效益。干细胞和原代组织的多个表观基因组图谱已经制作出来，并且已经建立了用于有效数据收集、处理和分析的管道。对于REMC项目，我们建议应用ChlP-Seq和HTBS管道来生成100种不同细胞类型的染色质状态和DNA甲基化的全面高分辨率地图。选择细胞类型是因为它们的生物学和医学重要性，以及它们最大限度地获得表观基因组数据的全面性的潜力。它们包括人类胚胎干细胞、胚胎干细胞衍生细胞、间充质干细胞、重编程干细胞和原代组织。ChlP-Seq将用于在每种细胞类型中绘制高信息量的染色质修饰和相关的染色质蛋白。HTBS将用于生成核苷酸分辨率的DNA甲基化图谱。参考表观基因组将揭示各种功能基因组元件的位置和激活状态，为研究细胞群体的发育状态和潜力提供信息，并为理解复杂的表观遗传调控机制提供框架。所有数据将在核实后提供给科学界。公共卫生相关性：表观遗传标记（“表观基因组”）的全面表征是对人类基因组在健康和疾病中的全球理解的关键一步。所提出的图谱研究将为人类表观遗传景观及其在细胞状态下的变化提供前所未有的视角，为表观遗传标记的功能和相互关系提供基本见解，并为未来正常和患病表观基因组的研究提供框架。

DESCRIPTION (provided by applicant): The Reference Epigenome Mapping Centers (REMC) will aim to transform our understanding of human epigenetics through production and integrative analysis of comprehensive reference epigenomes for ES cells, differentiated cells and tissues. In pursuit of this goal, we have assembled a unique scientific team and infrastructure with broad expertise and capabilities in stem cell biology, epigenomics, technology, production research and computation. We recently demonstrated two complementary methods that leverage ultra high-throughput sequencing for epigenomic analysis. In the first method, genome-wide chromatin maps are acquired by deep sequencing chromatin IP DNA (ChlP-Seq). In the second, nucleotide-resolution DNA methylation maps are generated by high-throughput bisulfite-sequencing (HTBS). These methods represent major improvements over prior tools as they yield precise digital information, have high genome coverage, require fewer cells and are cost-effective. Multiple epigenomic maps have already been produced for stem cells and primary tissues, and pipelines have been assembled for efficient data collection, processing and analysis. For the REMC project, we propose to apply ChlP-Seq and HTBS pipelines to generate comprehensive high-resolution maps of chromatin state and DNA methylation for 100 diverse cell types. Cell types were selected for their biological and medical importance, and for their potential to maximize the comprehensiveness of acquired epigenomic data. They include human ES cells, ES-derived cells, mesenchymal stem cells, reprogrammed stem cells and primary tissues. ChlP-Seq will be used to map highly informative chromatin modifications and related chromatin proteins in each cell type. HTBS will be used to generate nucleotide-resolution DNA methylation maps. Reference epigenomes will reveal the locations and activation states of diverse functional genomic elements, inform on the developmental state and potential of studied cell populations, and provide a framework for understanding complex epigenetic regulatory mechanisms. All data will be made available to the scientific community upon verification. PUBLIC HEALTH RELEVANCE: Comprehensive characterization of epigenetic marks ('the epigenome') is a critical step towards a global understanding of the human genome in health and disease. The proposed mapping studies will provide unprecedented views of the human epigenetic landscape and its variation across cell states, offer fundamental insight into the functions and interrelationships of epigenetic marks, and provide a framework for future studies of normal and diseased epigenomes.