Generating and Managing Large Scale Proteogenomic Data for ENCODE Cell Lines

描述(申请人提供)：第一个人类基因组序列于2001年发表，但到目前为止，也就是八年后的今天，主要问题仍然存在，例如基因组编码了多少基因，以及在这些基因中，有多少功能产物是由于选择性剪接等现象而编码的。国家人类基因组研究所(NHGRI)协调了DNA元件百科全书(ENCODE)项目，通过对人类基因组上的功能元件进行全面分类来回答这些问题。该项目的试点阶段详细研究了1%的基因组，揭示了广泛的转录，远远超出了经典基因模型所预测的范围。已发现的转录本中有很大一部分的生物学功能尚不清楚。ENCODE项目现在正在扩大规模，以检查整个人类基因组。结果很可能会与试点项目相呼应，揭示出广泛的转录，其中很大一部分具有未知的功能。蛋白质组学技术可以在一个称为蛋白质基因组图谱的过程中被应用，以确定无数转录本中的哪些编码蛋白质。这一方法已被用于揭示新基因、新的选择性剪接变体、新的起始点和上游开放阅读框架(ORF)。虽然在开发蛋白质组图谱技术方面取得了实质性进展，但利用蛋白质基因组学来协助ENCODE项目的一个重大障碍是缺乏与ENCODE转录图谱工作相协调的蛋白质组数据集。在这里，我们建议直接从转录工作研究的同一层I ENCODE细胞系中生成大规模蛋白质组数据集，将结果与转录映射工作协调起来，以确定哪些普遍存在的转录本被翻译。我们的具体目标是：1)使用最先进的质谱学方法在ENCODE细胞系上产生大规模的蛋白质组数据集；2)使用我们的数据库技术来存储、管理项目的所有结果，并使社区能够访问；3)使用我们的软件流水线将结果映射到最新的人类基因组草图，生成带有结果的UCSC(加州大学圣克鲁斯分校)基因组浏览器轨道。我们相信，结果将是关于我们的基因组及其编码的功能产品的知识的重大进步。 与公共卫生相关：人类基因组是人类生命和人类健康的蓝图，但我们还不了解它的语言--基因的语言。ENCODE项目正在系统地破译这种语言，这项提案的目标是通过揭示蓝图的哪些部分包含构建蛋白质的指令来加速这一努力。

DESCRIPTION (provided by applicant): The first human genome sequence was published in 2001, yet as of now, eight years later, major questions remain, such as how many genes are encoded by the genome, and of those genes, how many functional products are encoded due to phenomena like alternative splicing. The Encyclopedia of DNA Elements (ENCODE) project has been coordinated by National Human Genome Research Institute (NHGRI) to answer these questions by comprehensively classifying functional elements on the human genome. The pilot phase of the project studied 1% of the genome in detail, revealing extensive transcription well beyond that predicted by classical gene models. The biological function of a significant portion of the discovered transcripts is unclear. The ENCODE project is now scaling up to examine the whole human genome. It is likely that results will echo the pilot project, revealing extensive transcription, a significant fraction of which has unexplained function. Proteomic technologies can be applied, in a process called proteogenomic mapping, to determine which of the myriad transcripts encode proteins. This approach has been used to reveal new genes, new alternative splice variants, new start sites, and upstream open reading frames (ORFs). While substantive progress has been made in developing proteogenomic mapping technologies, a significant hurdle in using proteogenomics to assist with the ENCODE project is the lack of proteomic data sets that are coordinated with the ENCODE transcription mapping efforts. Here we propose to generate large-scale proteomic data sets directly from the same tier I ENCODE cell lines studied by the transcription efforts, coordinating the results with the transcription mapping efforts to determine which of the pervasive transcripts are translated. Our specific aims are to: 1) produce large scale proteomic data sets on ENCODE cell lines using the most advanced mass spectrometry methods, 2) use our database technologies to store, manage, and make accessible to the community all results of the project, and 3) use our software pipeline to map the results to the latest human genome drafts, producing a UCSC (University of California Santa Cruz) genome browser track with the results. We believe the result will be a significant advancement in knowledge about our genomes and the functional products they encode. PUBLIC HEALTH RELEVANCE: The human genome is the blueprint for human life and human health, but we do not yet understand its language - the language of genes. The ENCODE project is deciphering that language systematically, and the goal of this proposal is to accelerate that effort by revealing which parts of the blueprint contain instructions to build proteins.