Global Annotation of Regulatory Elements in the Human Genome

描述(申请人提供)：ENCODE项目的目标是通过描绘组成所有基因的DNA序列特征，包括外显子、内含子、启动子和顺式调控序列，为科学界提供完整的人类基因组注释。ENCODE试点项目试图开发和测试各种实验、计算和分析平台，以确定通过关注人类基因组的1%来解决这个问题的最佳方法。在ENCODE的这一初始阶段，该提案的申请者开发了强大的高通量方法来检测和验证试点区域中的功能转录启动子、DNA甲基化模式和转录因子的占有率，并证明这些方法可以完全扩展到整个人类基因组，具有高度的稳健性、敏感性和特异性。这些经验，加上由此产生的技术和分析平台以及现有的高效基础设施，导致了对NHGRI的RFA-HG-07-030的响应。这项申请提出了一项雄心勃勃的计划，旨在扩大一个计划，以绘制和功能注释人类基因组的顺式调控序列。该计划强调三条实验管道的全基因组全面性：1)一种名为ChlPSeq的新方法，用于阐明600多种综合转录因子：DNA相互作用；2)一种类似的新方法，名为MethSeq，用于确定人类基因组中所有CpG丰富区域在1,000多种人类细胞类型和细胞状态中的甲基化状态；以及3)一条高通量转基因管道，用于测量25,000个人类“启动子+”近端顺式调节域的转录活性，其中包括每个注释蛋白编码基因的至少一个主要启动子。启动子管道的第二个主要产品将是所有人类基因的最接近报告构建的物理资源，旨在适应未来对启动子调控基序的精细结构剖析和长距离元件的测试。这个项目中的所有实验工作都将接受适当的质量衡量标准的分析。此外，比较基因组学和其他计算分析将与实验成果相结合，以帮助确定管道输入的优先顺序和形状，并以对生物学家和基因学家都有用的形式获取信息。这些分析将产生几个大规模的可交付成果，包括数百个芯片数据驱动的序列基序模型，其中一些额外利用了数百个转录因子中每一个的进化保守。

DESCRIPTION (provided by applicant): The goal of the ENCODE Project is to provide the scientific community with a complete annotation of the human genome by delineating the DNA sequence features that comprise all genes, including exons, introns, promoters and cis-regulatory sequences. The pilot ENCODE project sought to develop and test a variety of experimental, computational and analytical platforms to determine the best ways to approach this problem by focusing on a defined 1% of the human genome. During this initial phase of ENCODE, the applicants of this proposal developed robust high-throughput methods for detecting and validating functional transcription promoters, DNA methylation patterns, and transcription factor occupancy in the pilot regions, and demonstrated that these approaches can be scaled fully to the entire human genome with high robustness, sensitivity and specificity. These experiences, together with the resulting technology and analysis platforms and an existing, highly productive infrastructure, lead to this response to NHGRI's RFA-HG-07-030. This application presents an ambitious proposal to expand a program to map and functionally annotate cis-regulatory sequences of the human genome. The plan emphasizes full genome-comprehensivity for three experimental pipelines.: 1) a new sequence-based method called ChlPSeq to elucidate more than 600 comprehensive transcription factor:DNA interactomes; 2) a similar new method called MethSeq to determine the methylation status of all the CpG-rich regions in the human genome in more than 1,000 human cell types and cell states; and 3) a high throughput transfection assay pipeline to measure transcriptional activities of 25,000 human "promoter-plus" proximal cis-regulatory domains, including at least one major promoter for each of the annotated protein-coding genes. A second major product of the promoter pipeline will be a physical resource of proximate reporter constructs for all human genes, designed to accommodate future fine-structure dissection of the promoter regulatory motifs and testing of long-distance elements. All of the experimental work in this project will be subjected to analysis with appropriate quality metrics. In addition, comparative genomics and other computational analyses will be integrated with the experimental production to help prioritize and shape input to the pipelines and to capture information in forms useful to both biologists and genomicists. These analyses will produce several large-scale deliverables, including hundreds of ChIP data-driven sequence motif models, some of which additionally leverage evolutionary conservation for each of hundreds of transcription factors.