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.

翻译是将信使RNA中编码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了蛋白质合成的时间尺度，影响细胞中蛋白质分子的丰度，并且最近已证明会影响产生的蛋白质的结构和功能。这些速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工具，以测量从下一代测序技术核糖体分析（Ribo-Seq）生成的实验数据中的翻译定型和 - 延长速率。物理生物信息学为生物信息学领域带来了物理科学的观点，并允许从大型生物学数据集中提取更多的信息。将创建新的分析方法，以衡量Ribo-Seq和其他数据的翻译启动和伸长率的绝对速率，从而使实验者可以测量这些数量。该项目将通过确定伸长阶段对全球和单基因水平的翻译控制的贡献，以及进化编码的翻译 - 延细动力学的变化是否会调节伴侣结合，从而促进分子生物学的知识。将举行网络研讨会和研讨会，将生物信息学家介绍该项目中开发的方法，运行分析管道并解释结果的理论，从而增强了研究基础架构。这些事件将被记录并公开存档，以供社区使用。作为对服务不足的K-12社区的推广的一部分，该项目将通过宾夕法尼亚州立大学的向上约束数学和科学计划向少数民族高中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从事大学研究经验。跨夏季，很难在跨生物体的转录率跨跨夏季进行大学研究经验。该项目的目的是开发和应用植根于化学和物理领域的物理生物信息学分析方法，以测量从下一代测序技术Ribo-Seq产生的实验数据中的翻译引入和 - 延长速率。可以肯定的是，文献中已经报道了利用启发式或基于仿真方法的这些速率的定性措施。但是，这些方法通常不会产生绝对速率，也不能保证提供最佳的解决方案。绝对率的知识是必不可少的，因为它们是系统中的实际速率，并且可以确定它们对其他共译过程的影响。翻译涉及分子和化学反应，这意味着与化学定律和物理定律一致的分析方法更有可能产生准确的结果。利用理论化学，物理和生物信息学方面的跨学科专业知识，PI的实验室将在该项目中开发方法：（1）最佳地确定核糖体A位置对核糖体保护片段的位置，该片段是由Ribo-Seq实验产生的，是核心seq实验的第一步 - 迈向测量绝对率的第一步； （2）通过将翻译视为离散流体流量的一种形式，从核糖体径流实验中测量平均密码子翻译速率； （3）测量稳态核糖实验的单个密码子翻译速率； （4）通过Ribo-Seq，RNA-Seq和多核体分析数据的组合来测量起始率。这些方法将应用于回答基本生物学问题：在转化的起始与伸长阶段确定的基因表达的翻译控制在多大程度上？进化编码的翻译 - 延细动力学是否与伴侣结合有因果关系影响伴侣结合？这些问题的答案将提供有关在翻译阶段如何调节基因表达方式的基本问题的洞察力，当基因表达在某些疾病中出现问题时，可能会为新的治疗方法开放新的治疗途径。该奖项反映了NSF的法定任务，并被认为是通过基金会的知识分子和更广泛影响的评估来评估CRITERIA CRITERIA CRITERIA的评估。

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.