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

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.