Toward a comprehensive functional annotation of the human genome

ENCODE项目的目标是为生物医学界提供一个完整的和生物学上可解释的人类基因组注释。这意味着发现和定位所有基因的所有部分，包括外显子、内含子、启动子和顺式调控序列，在ENCODE项目的前几个阶段，该提案的申请人开发并应用了稳健的、高通量的、全基因组的方法，用于确定转录因子占有率、评估DNA甲基化、鉴定RNA转录本以及实验测试候选调控元件和突变。来自前几个阶段的经验与所产生的技术和分析平台以及申请人现有的高效基础设施相结合，形成了对NHGRI RFA-HG-11-024（“在人类和模式生物中扩展DNA元素百科全书（ENCODE）”）的回应的基础。该申请提出了一个雄心勃勃的建议，即扩大ENCODE的生物学维度，以包括基本上所有用于测量占用率的转录因子，并从数百种非常特定的细胞类型甚至单细胞中产生转录组。具体计划是：1）在两种或更多种细胞类型中以高分辨率确定所有转录因子和主要辅因子的全基因组占有率; 2）在超过300种明确定义的未培养细胞类型中绘制和定量所有信使RNA转录物、微小RNA和其他非核糖体RNA; 3）在超过300种细胞类型中以核苷酸分辨率绘制全基因组DNA甲基化状态;和4）应用高通量瞬时转染测定系统来测试约2，000个候选调控元件对基因调控的影响。该项目的所有实验工作将通过适当的质量指标进行评估，经过质量控制，所有数据将迅速存入可免费访问的基因组数据库。此外，计算分析，包括比较和群体基因组学数据的评估，将与实验生产相结合，以帮助确保质量，并以生物学家，基因组学家和医学研究人员有用的形式捕获信息。这些特定目标的完成将使生物医学研究人员能够更好、更快地了解基因组疾病（包括癌症、心血管疾病和几乎所有常见疾病）突变的后果，从而更充分地实现基因组学对人类健康的影响。

The goal of the ENCODE Project is to provide the biomedical community with a complete and biologically interpretable annotation of the human genome. This means discovering and mapping all parts of all genes, including exons, introns, promoters and cis-regulatory sequences, in previous phases of the ENCODE Project, the applicants of this proposal developed and applied robust, high-throughput, genome-wide methods for determining transcription factor occupancy, assessing DNA methylation, identifying RNA transcripts, and experimentally testing candidate regulatory elements and mutations. The combination of experiences from the previous phases with the resulting technology and analysis platforms and the existing, highly productive infrastructure of the applicants form the basis of this response to NHGRI's RFA-HG-11-024 ("Expanding the Encyclopedia of DNA Elements (ENCODE) in the Human and Model Organisms"). This application presents an ambitious proposal to expand the biological dimensions of ENCODE to include essentially all transcription factors for measurements of occupancy and to produce transcriptomes from hundreds of very specific cell types, and even single cells. The specific plan is to: 1) determine genome wide occupancy for all transcription factors and major cofactors with high resolution in two or more cell types; 2) map and quantify all messenger RNA transcripts, microRNAs and other non-ribosomal RNAs in more than 300 well-defined, uncultured cell types; 3) map DNA methylation state genome-wide at nucleotide resolution in more than 300 cell types; and 4) apply a high-throughput transient transfection assay system to test the impact of -2,000 candidate regulatory elements on gene regulation. All experimental work in this project will be evaluated by appropriate quality metrics, and after quality control, all data will be rapidly deposited in publi, freely accessible genome databases. In addition, computational analyses, including evaluation of comparative and population genomics data, will be integrated with the experimental production to help ensure quality and to capture information in forms useful to biologists, genomicists, and medical researchers. Completion of these Specific Aims will enable biomedical researchers to better and more rapidly understand the consequences of mutations in genomic disorders, including cancer, cardiovascular disease, and almost ail common diseases and, therefore, to more fully realize the potential of genomics to impact human health.