Mapping the first half of the REFERENCE human binary protein interactome

绘制参考人类二元蛋白质相互作用组的前半部分

• 批准号: 8666559
• 负责人: David E. Hill
• 金额: $ 181.41万
• 依托单位: DANA-FARBER CANCER INST
• 依托单位国家: 美国
• 财政年份: 1998
• 资助国家: 美国
• 起止时间: 1998-07-01 至 2015-09-23
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8666559
• 关键词: Address; Animal Model; Beryllium; Biological; Biological Process; Biology; Biomedical Research; Cell Line; Cells; Code; Collaborations; Complement; Complex; Cosmids; DNA; DNA Sequence; Data; Data Quality; Data Set; Development; Disease; Enzymes; Fluorescence; Genes; Genome; Genotype; Goals; Grant; Hand; Human; Human Genome; Lasers; Literature; Maps; Methods; Modeling; Nature; Network-based; Open Reading Frames; Organism; Paper; Phase; Phenotype; Play; Process; Protein-Protein Interaction Map; Proteins; Proteome; Publishing; RNA; Resources; Role; Science; Scientist; Systems Biology; Technology; Testing; Therapeutic Intervention; Time; Tissues; Work; YAC Clone; base; complex biological systems; cost; gene cloning; genome sequencing; improved; in vivo; innovation; insight; macromolecule; next generation sequencing; predictive modeling; protein protein interaction; scaffold

DESCRIPTION (provided by applicant): Complex biological systems and cellular networks underlie most genotype to phenotype relationships. In the last decade, basic concepts of network biology have been described, emphasizing why cellular networks are important to consider in biology. Importantly, it is becoming increasingly clear that more high quality empirically derived datasets are needed to better describe biological networks and genotype to phenotype relationships. The interactome of an organism is the network formed by the complete set of interactions that can occur in a physiologically relevant dynamic range between all its macromolecules, including protein-protein, DNA-protein, RNA-protein, and RNA-RNA interactions. In this proposal, we focus on high-throughput (HT), proteome-scale mapping of what we refer to as the REFERENCE human binary protein-protein interactome network map. Major innovations in this application enable to define a clear roadmap for completion of this REFERENCE map by the end of this decade. During this coming cycle, we will expand the human HT binary interactome map from ~15% coverage, which is the milestone of the current cycle, to ~50%. We will also briefly discuss how we foresee further expansion to near completeness thereafter. The accumulation of DNA sequencing data exploded for the Human Genome Sequencing project in the 1990s when four crucial elements were assembled: i) cosmids, BAC, and YAC clone resources covering most of the genome; ii) automated laser-fluorescence sequencing, iii) the PHRED score used to systematically assess sequencing data quality, and iv) the development of "hands-off" automated experimental steps. We describe below how the human binary interactome mapping project is reaching a similarly exploding phase: i) having significantly contributed to the ORFeome Collaboration (OC) we now have a nearly complete protein-coding ORF clone resource, ii) we developed a new strategy to apply the power of next-generation sequencing to interactome mapping, iii) we have published a new empirical framework that systematically assess interactome mapping data quality, and iv) we will describe new "hands-off" automated strategies that greatly increase throughput and decrease cost. Our specific aims are: i) to expand human binary interactome mapping to a full complement of protein-coding genes cloned by OC, ii) to reach ~50% coverage of the REFERENCE human binary interactome network map, and iii) to expand global network analyses of our newly mapped human binary interactome network.

描述(由申请人提供)：复杂的生物系统和细胞网络构成了大多数基因与表型关系的基础。在过去的十年里，描述了网络生物学的基本概念，强调了为什么细胞网络在生物学中是重要的考虑因素。重要的是，越来越清楚的是，需要更高质量的经验性数据集来更好地描述生物网络和基因与表型的关系。生物体的相互作用组是指所有大分子之间在生理上相关的动态范围内发生的一整套相互作用形成的网络，包括蛋白质-蛋白质、DNA-蛋白质、RNA-蛋白质和RNA-RNA相互作用。在这项建议中，我们关注高通量(HT)，蛋白质组规模的作图，我们称之为参考人类二元蛋白质-蛋白质相互作用组网络图。这项应用的主要创新使我们能够确定一个明确的路线图，以便在本十年结束前完成这一参考地图。在即将到来的这个周期中，我们将把人类HT二元互作组图的覆盖率从本周期的里程碑~15%扩大到~50%。我们还将简要讨论我们如何预见今后进一步扩大到接近完成。20世纪90年代，人类基因组测序项目的DNA测序数据的积累出现了爆炸性增长，当时组装了四个关键元素：i)覆盖大部分基因组的Cosmids、BAC和YAC克隆资源；ii)自动化激光荧光测序；iii)用于系统评估测序数据质量的Phred评分；以及iv)开发“不插手”的自动化实验步骤。下面我们描述人类二元互作组图项目是如何达到类似的爆炸性阶段：i)对ORFeome协作(OC)做出了重大贡献，我们现在拥有了几乎完整的蛋白质编码ORF克隆资源，ii)我们开发了一种新的策略，将下一代测序的能力应用到互作组图中，iii)我们已经发表了一个新的经验框架，系统地评估了互作组图的数据质量，以及iv)我们将描述新的“不插手”自动化策略，这些策略大大提高了吞吐量和降低了成本。我们的具体目标是：i)将人类二元互作组图扩展到OC克隆的完整的蛋白质编码基因；ii)使参考的人二元互作组网络图的覆盖率达到~50%；iii)扩大我们新绘制的人二元互作组网络的全球网络分析。

项目成果

The Development of RNA-KISS, a Mammalian Three-Hybrid Method to Detect RNA-Protein Interactions in Living Mammalian Cells.

RNA-KISS 的开发，一种用于检测活哺乳动物细胞中 RNA-蛋白质相互作用的哺乳动物三杂交方法。

• DOI: 10.1021/acs.jproteome.0c00068
• 发表时间: 2020
• 期刊: Journal of proteome research
• 影响因子: 4.4
• 作者: Lemmens,Irma;Jansen,Sander;deRouck,Steffi;deSmet,Anne-Sophie;Defever,Dieter;Neyts,Johan;Dallmeier,Kai;Tavernier,Jan
• 通讯作者: Tavernier,Jan

MECP2 Is a Frequently Amplified Oncogene with a Novel Epigenetic Mechanism That Mimics the Role of Activated RAS in Malignancy.

• DOI: 10.1158/2159-8290.cd-15-0341
• 发表时间: 2016-01
• 期刊: Cancer discovery
• 影响因子: 28.2
• 作者: Neupane M;Clark AP;Landini S;Birkbak NJ;Eklund AC;Lim E;Culhane AC;Barry WT;Schumacher SE;Beroukhim R;Szallasi Z;Vidal M;Hill DE;Silver DP
• 通讯作者: Silver DP

Multiplex single-molecule interaction profiling of DNA-barcoded proteins.

• DOI: 10.1038/nature13761
• 发表时间: 2014-11-27
• 期刊: NATURE
• 影响因子: 64.8
• 作者: Gu, Liangcai;Li, Chao;Aach, John;Hill, David E.;Vidal, Marc;Church, George M.
• 通讯作者: Church, George M.