RNA-seq analysis on the PTH deficient cells

In the early stage of translation elongation, peptidyl-tRNA (pep-tRNA) with short nascent chain frequently dissociates from the ribosome (pep-tRNA drop-off). Inactivation of PTH (peptidyl-tRNA hydrolase) causes rapid accumulation of pep-tRNAs and depletion of aminoacyl(aa)-tRNAs, leading to defective protein synthesis. We established a highly sensitive method for direct profiling of pep-tRNAs accumulated in the cell and identified more than 700 peptide sequences of the pep-tRNAs. To characterize codon preference at the drop-off sites for the pep-tRNAs, we carried out RNA-seq on the PTH deficient cells to obtain the transcriptome profile.