ABI INNOVATION: Physical Bioinformatics Tools for Measuring Translation Rates from Next-Generation Sequencing Data

ABI 创新：用于测量下一代测序数据翻译率的物理生物信息学工具

• 批准号: 1759860
• 负责人: Edward O'Brien
• 金额: $ 68.79万
• 依托单位: Pennsylvania State Univ University Park
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-07-15 至 2023-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1759860&HistoricalAwards=false
• 关键词: ABI; INNOVATION; Physical; Bioinformatics; Tools

Translation is the process by which the genomic information encoded in a messenger RNA is converted into a protein molecule. The rates associated with translation determine the time scales of protein synthesis, influence the abundance of protein molecules in cells, and have recently been shown to influence the structure and function of the protein produced. These rates are difficult to measure across the transcriptomes of organisms. The purpose of this project is to develop and apply physical bioinformatics analysis tools to measure translation-initiation and -elongation rates from experimental data generated with the next-generation sequencing technique Ribosome Profiling (Ribo-Seq). Physical Bioinformatics brings a physical-science perspective to the field of bioinformatics and permits more information to be extracted from big biological data sets than previously possible. New analysis methods will be created to measure absolute rates of translation initiation and elongation from Ribo-Seq and other data, making it possible for experimentalists to measure these quantities. This project will advance knowledge in molecular biology by determining the contribution of the elongation phase to translation control at both the global and single-gene level and whether changes in evolutionarily encoded translation-elongation kinetics modulates chaperone binding. Webinars and workshops will be held to introduce bioinformaticians to the theory underlying the methods developed in this project, running the analysis pipelines, and interpreting the results - thereby enhancing research infrastructure. These events will be recorded and publicly archived for future use by the community. As part of outreach to underserved K-12 communities, this project will introduce minority high school students to scientific research in Bioinformatics through Penn State's Upward Bound Math and Science program, which arranges for these students to engage in university research experience over the summer.Translation initiation and elongation rates are difficult to measure across the transcriptomes of organisms. The purpose of this project is to develop and apply physical bioinformatics analysis methods, rooted in the fields of chemistry and physics, to measure translation-initiation and -elongation rates from experimental data generated with the Next-Generation Sequencing technique Ribo-Seq. To be sure, qualitative measures of these rates utilizing heuristic or simulation-based approaches have been reported in the literature. However, these methods often do not yield absolute rates nor are they guaranteed to provide optimal solutions. Knowledge of absolute rates is essential because they are the actual rates in the system, and by knowing them their impact on other co-translational processes can be determined. Translation involves molecules and chemical reactions, meaning that analysis methods consistent with the laws of chemistry and physics are more likely to yield accurate results. Utilizing the interdisciplinary expertise in theoretical chemistry, physics, and bioinformatics, the PI's lab will develop methods in this project that: (1) optimally identify the location of the ribosome's A-site on ribosome-protected fragments generated from Ribo-Seq experiments - the first step towards measuring absolute rates; (2) measure the average codon translation rates from ribosome run-off experiments by treating translation as a form of discretized fluid flow; (3) measure individual codon translation rates from steady-state Ribo-Seq experiments; (4) measure initiation rates through a combination of Ribo-Seq, RNA-Seq and polysome profiling data. The methods will be applied to answer fundamental biological questions: To what extent is translation control of gene expression determined in the initiation versus elongation phase of translation? Do evolutionarily encoded translation-elongation kinetics that correlate with chaperone binding causally influence chaperone binding? Answers to these questions will provide insight into fundamental issues concerning how gene expression is regulated at the stage of translation, and may open new avenues for treatment when gene expression goes awry in some diseases.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

翻译是将编码在信使RNA中的基因组信息转化为蛋白质分子的过程。与翻译相关的速率决定蛋白质合成的时间尺度，影响细胞中蛋白质分子的丰度，并且最近已被证明影响所产生的蛋白质的结构和功能。这些比率很难在生物体的转录组中测量。本项目的目的是开发和应用物理生物信息学分析工具，从下一代测序技术Ribosome Profiling（Ribo-Seq）产生的实验数据中测量断裂起始和延伸率。物理生物信息学为生物信息学领域带来了物理科学的视角，并允许从大生物数据集中提取比以前更多的信息。将创建新的分析方法来测量Ribo-Seq和其他数据的翻译起始和延伸的绝对速率，使实验人员能够测量这些量。该项目将通过确定延伸阶段在全球和单基因水平上对翻译控制的贡献以及进化编码的延伸-延伸动力学的变化是否调节分子伴侣结合来推进分子生物学知识。将举行网络研讨会和研讨会，向生物信息学家介绍该项目开发的方法的理论基础，运行分析管道，并解释结果-从而加强研究基础设施。这些活动将被记录并公开存档，供社区将来使用。作为服务不足的K-12社区的外展活动的一部分，该项目将通过宾夕法尼亚州立大学的向上绑定数学和科学计划向少数民族高中学生介绍生物信息学的科学研究，该计划安排这些学生在夏季参与大学研究体验。翻译起始和延伸率很难在生物体的转录组中测量。该项目的目的是开发和应用物理生物信息学分析方法，植根于化学和物理领域，从下一代测序技术Ribo-Seq产生的实验数据中测量断裂起始和延伸率。可以肯定的是，定性措施，这些利率利用启发式或基于模拟的方法已在文献中报道。然而，这些方法通常不产生绝对速率，也不能保证提供最佳解决方案。绝对速率的知识是必不可少的，因为它们是系统中的实际速率，通过了解它们，可以确定它们对其他共翻译过程的影响。翻译涉及分子和化学反应，这意味着符合化学和物理定律的分析方法更有可能产生准确的结果。利用理论化学，物理学和生物信息学的跨学科专业知识，PI的实验室将在本项目中开发方法：（1）最佳地确定核糖体A位点在Ribo-Seq实验产生的核糖体保护片段上的位置-测量绝对速率的第一步;（2）通过将翻译处理为离散流体流的形式，测量来自核糖体流出实验的平均密码子翻译速率;（3）从稳态Ribo-Seq实验测量单个密码子翻译速率;（4）通过Ribo-Seq、RNA-Seq和多核糖体分析数据的组合测量起始速率。这些方法将被应用于回答基本的生物学问题：在何种程度上是翻译控制的基因表达决定在启动与延伸阶段的翻译？与伴侣结合相关的进化编码的伸展-伸长动力学是否会因果地影响伴侣结合？这些问题的答案将有助于深入了解基因表达在翻译阶段是如何调节的基本问题，并可能为某些疾病中基因表达出错的治疗开辟新的途径。该奖项反映了NSF的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

项目成果

A chemical kinetic basis for measuring translation initiation and elongation rates from ribosome profiling data

• DOI: 10.1371/journal.pcbi.1007070
• 发表时间: 2018-12
• 期刊: PLoS Computational Biology
• 影响因子: 4.3
• 作者: Ajeet K. Sharma;Pietro Sormanni;Nabeel Ahmed;P. Ciryam;Ulrike A. Friedrich;G. Kramer;E. O’Brien

Electrostatic Interactions Govern Extreme Nascent Protein Ejection Times from Ribosomes and Can Delay Ribosome Recycling

• DOI: 10.1021/jacs.9b12264
• 发表时间: 2020-04-01
• 期刊: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
• 影响因子: 15
• 作者: Nissley, Daniel A.;Vu, Quyen V.;O'Brien, Edward P.
• 通讯作者: O'Brien, Edward P.

Identifying A- and P-site locations on ribosome-protected mRNA fragments using Integer Programming

• DOI: 10.1038/s41598-019-42348-x
• 发表时间: 2019-04-18
• 期刊: SCIENTIFIC REPORTS
• 影响因子: 4.6
• 作者: Ahmed, Nabeel;Sormanni, Pietro;O'Brien, Edward P.
• 通讯作者: O'Brien, Edward P.