Pavlov et al. 2021 (PRJNA607566)

Title	Estimation of peptide elongation times from ribosome profiling spectra
Organism
Number of Samples	3
Release Date	2020/02/19 00:00
Sequencing Types
Protocol Details

GWIPS-viz	Trips-Viz

Title
Authors	Pavlov MY,Ullman G,Ignatova Z,Ehrenberg M
Journal	Nucleic acids research
Publication Date	2021 May 21
Abstract	Ribosome profiling spectra bear rich information on translation control and dynamics. Yet, due to technical biases in library generation, extracting quantitative measures of discrete translation events has remained elusive. Using maximum likelihood statistics and data set from Escherichia coli we develop a robust method for neutralizing technical biases (e.g. base specific RNase preferences in ribosome-protected mRNA fragments (RPF) generation), which allows for correct estimation of translation times at single codon resolution. Furthermore, we validated the method with available datasets from E. coli treated with antibiotic to inhibit isoleucyl-tRNA synthetase, and two datasets from Saccharomyces cerevisiae treated with two RNases with distinct cleavage signatures. We demonstrate that our approach accounts for RNase cleavage preferences and provides bias-corrected translation times estimates. Our approach provides a solution to the long-standing problem of extracting reliable information about peptide elongation times from highly noisy and technically biased ribosome profiling spectra. © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.
PMC	PMC8136808
PMID	33885812
DOI

ⓘ For more Information on the columns shown here see: About