Measuring Translation Efficiency by RNA Immunoprecipitation of Translation Initiation Factors

Eukaryotic mRNAs are bound by a multitude of RNA binding proteins (RBPs) that control their localization, transport, and translation. Measuring the rate of translation of mRNAs is critical for understanding the factors and pathways involved in gene expression. In this chapter, we present a method to compare the rate of translation of individual mRNA species based on the fraction of mRNA bound by a specific ribonucleoprotein involved in the general translation machinery. The ribonucleoprotein complex is immunoprecipitated using an antibody for the RBP, followed by RT-PCR to semi-quantitatively determine the amount of an individual mRNA fraction bound by a translation regulating protein such as eIF4E.