Our current understanding of the adaptive effects of mutation is largely limited to alterations in protein coding sequence and disruption of transcriptional cis-regulatory promoters. Very little is known about how mutations alter translation, or the role these mutations play in adaptation and evolution. This project seeks to address this gap by identifying the functional effect of mutations on translation. To accomplish this I will first identify mutations that arise from adaptation to various nutrient limited environments. I will then use expression profiling (e.g. RNA-seq, ribosome profiling, and RATE-seq) to identify the effect these mutations have on translation, as well as other levels of gene expression. This will provide insight into the magnitude of effect mutations have on translation and their relative rate. Furthermore, to fully characterize the role synonymous mutations have on fitness I will be using a deep scanning synonymous mutation library. To understand the role tRNA abundance plays in the fitness effect of a given synonymous mutations, I will also be evaluating fitness within tRNA under- and over-expression backgrounds. Because of the closely coupled nature of translation rates and mRNA decay, I will also characterize the effect synonymous mutations have on mRNA decay using RATE-seq. My analysis of the functional effects of these mutations on gene expression, particularly within the genetic background and environment in which they arose, will allow for the development of a machine learning algorithm that can use sequence and annotation features to predict the effect of a mutation on gene expression. This tool will aid future research into the effect mutations have of gene expression by allowing the identification of high-confidence candidates for further evaluation. This project will be conducted at New York University?s Center for Genomics and Systems Biology, whose mission is to answer otherwise intractable biological questions using applied experimental and computational approaches. The Center houses numerous facilities and cores that will be instrumental in the performance of this work. The collaborative atmosphere and multi-disciplinary nature of NYU?s research communities that will enable me to stay abreast of developments in related fields and to rapidly communicate my research to interested parties. I will be trained under the guidance of Dr. David Gresham, an excellent researcher working on complementing long-term evolution experiments with gene expression studies to characterize the adaptive potential of the regulation of gene expression.
The translation of mRNA into protein is a critical step in gene expression that is tightly regulated with mis-regulation of translation being a hallmark of many human pathologies. Understanding how mutations can alter the regulation of translation is an understudied but important aspect of adaptation and evolution. Ultimately, without an understanding of the adaptive potential of translation we have an incomplete, and imperfect, picture of the underlying genetic causes of numerous forms of cancer and genetic diseases.
