Experimental And Computational Analysis of Mmamalian mRNAs: Translatibility and Plasticity
Authors: Yuan Qiao 1, Stefan Chirostov 2, Silpa Goriparthi 1, Xiaojuan Zheng 1, Brian LePore 2, Osman Yasar 2, and Huseyin Aktas 1
- Harvard University Medical School
- SUNY Brockport, Department of Computational Science
Abstract
Translation of mRNAs into proteins is one leg of the central dogma of biology and plays a central role in the regulation of cell proliferation, differentiation, and survival. Translation is divided into initiation, elongation and termination phases each governed by unique set of multi-protein complexes, with initiation as the major site of regulation in eukaryotes. Individual mRNAs are translated with the varying efficiencies that further varies depending on cellular context. Regulated translation initiation plays a critical role in maintaining physiologic control on cell proliferation and cytoprotection from cellular stress. Inability to regulate gene expression at the level of translation initiation is contributes to development of cancer and metabolic syndrome, a term that includes obesity, arteriosclerosis, and type II diabetes.
Translational efficiency of mRNAs is determined by the inherent properties of mRNAs and their interaction with cellular factors such as sequence specific RNA binding proteins. The most studied inherent properties mRNAs that impinge on the translational efficiency are the sequences surrounding the initiator AUG codon (the Kozak consensus), the length and complexity of 5' untranslated region (UTR) and presence of upstream open reading frames (uORF) or upstream initiator (uAUG) codons. From the evolutionary point the most abundant proteins, housekeeping proteins, should be coded for by strong mRNAs to reduce the cost of transcribing them while most regulatory proteins should be coded for by weak mRNAs so that an additional level of control can be imposed on their expression. Yet another class of mRNAs should be translated efficiently only under very specific conditions, when their protein product would be needed to deal with cellular "emergiencies". Since the cost of maintaining large numbers of sequence specific RNA binding proteins to regulate translation of many thousands of mRNAs under different patho/physiologic conditions would be too great a burden, we hypothesized that inherent properties of mRNAs may be responsible for bulk of translational regulation. To test this hypothesis, we undertook a genome-wide study to determine the strength of mammalian mRNAs by assigning a translatability score to each mRNA based on the Kozak consensus sequence around the initiator AUG, length and complexity of 5'UTR, presence and context uORF and uAUGs and likely hood of coding for multiple proteins. We initially wrote a software program that utilized published experimental data and statistical approaches to determine strength of mRNAs assuming a linear scanning model for translation initiation. To confirm and if necessary refine this model we generated several hundred artificial reporter mRNA and expressed them in the mammalian cells. We refined our model based on this data. In this communication we will report on the translatability of mammalian mRNAs on a genome-wide scale. Data mining tools are being developed to utilize genomic and proteomic databases to further validate and refine this model.