High-Resolution Ribosome Profiling for Determining Ribosome Functional States During Translation Elongation

Translation elongation is a highly choreographed process that involves substantial conformational changes of the ribosome to accommodate aminoacyl-tRNAs and traverse along the mRNA template. To capture distinct functional states of the ribosome, a high-resolution ribosome profiling-based approach has been developed. By deep-sequencing differently sized ribosome-protected mRNA fragments, this approach captures not only ribosome positions but also their functional states in vivo across the Saccharomyces cerevisiae transcriptome with codon resolution. This chapter presents a condensed and step-by-step protocol for preserving ribosomes in their functional states using a cocktail of antibiotics that traps distinct steps of elongating ribosomes and for constructing a cDNA library derived from the ribosome-protected mRNA fragments for deep sequencing.