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choros: correction of sequence-based biases for accurate quantification of ribosome profiling data

Ribosome profiling quantifies translation genome-wide by sequencing ribosome-protected fragments, or footprints. Its single-codon resolution allows identification of translation regulation, such as ribosome stalls or pauses, on individual genes. However, enzyme preferences during library preparation...

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Autores principales: Mok, Amanda, Tunney, Robert, Benegas, Gonzalo, Wallace, Edward W. J., Lareau, Liana F.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9980091/
https://www.ncbi.nlm.nih.gov/pubmed/36865295
http://dx.doi.org/10.1101/2023.02.21.529452
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author Mok, Amanda
Tunney, Robert
Benegas, Gonzalo
Wallace, Edward W. J.
Lareau, Liana F.
author_facet Mok, Amanda
Tunney, Robert
Benegas, Gonzalo
Wallace, Edward W. J.
Lareau, Liana F.
author_sort Mok, Amanda
collection PubMed
description Ribosome profiling quantifies translation genome-wide by sequencing ribosome-protected fragments, or footprints. Its single-codon resolution allows identification of translation regulation, such as ribosome stalls or pauses, on individual genes. However, enzyme preferences during library preparation lead to pervasive sequence artifacts that obscure translation dynamics. Widespread over- and under-representation of ribosome footprints can dominate local footprint densities and skew estimates of elongation rates by up to five fold. To address these biases and uncover true patterns of translation, we present choros, a computational method that models ribosome footprint distributions to provide bias-corrected footprint counts. choros uses negative binomial regression to accurately estimate two sets of parameters: (i) biological contributions from codon-specific translation elongation rates; and (ii) technical contributions from nuclease digestion and ligation efficiencies. We use these parameter estimates to generate bias correction factors that eliminate sequence artifacts. Applying choros to multiple ribosome profiling datasets, we are able to accurately quantify and attenuate ligation biases to provide more faithful measurements of ribosome distribution. We show that a pattern interpreted as pervasive ribosome pausing near the beginning of coding regions is likely to arise from technical biases. Incorporating choros into standard analysis pipelines will improve biological discovery from measurements of translation.
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spelling pubmed-99800912023-03-03 choros: correction of sequence-based biases for accurate quantification of ribosome profiling data Mok, Amanda Tunney, Robert Benegas, Gonzalo Wallace, Edward W. J. Lareau, Liana F. bioRxiv Article Ribosome profiling quantifies translation genome-wide by sequencing ribosome-protected fragments, or footprints. Its single-codon resolution allows identification of translation regulation, such as ribosome stalls or pauses, on individual genes. However, enzyme preferences during library preparation lead to pervasive sequence artifacts that obscure translation dynamics. Widespread over- and under-representation of ribosome footprints can dominate local footprint densities and skew estimates of elongation rates by up to five fold. To address these biases and uncover true patterns of translation, we present choros, a computational method that models ribosome footprint distributions to provide bias-corrected footprint counts. choros uses negative binomial regression to accurately estimate two sets of parameters: (i) biological contributions from codon-specific translation elongation rates; and (ii) technical contributions from nuclease digestion and ligation efficiencies. We use these parameter estimates to generate bias correction factors that eliminate sequence artifacts. Applying choros to multiple ribosome profiling datasets, we are able to accurately quantify and attenuate ligation biases to provide more faithful measurements of ribosome distribution. We show that a pattern interpreted as pervasive ribosome pausing near the beginning of coding regions is likely to arise from technical biases. Incorporating choros into standard analysis pipelines will improve biological discovery from measurements of translation. Cold Spring Harbor Laboratory 2023-02-22 /pmc/articles/PMC9980091/ /pubmed/36865295 http://dx.doi.org/10.1101/2023.02.21.529452 Text en https://creativecommons.org/licenses/by/4.0/This work is licensed under a Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/) , which allows reusers to distribute, remix, adapt, and build upon the material in any medium or format, so long as attribution is given to the creator. The license allows for commercial use.
spellingShingle Article
Mok, Amanda
Tunney, Robert
Benegas, Gonzalo
Wallace, Edward W. J.
Lareau, Liana F.
choros: correction of sequence-based biases for accurate quantification of ribosome profiling data
title choros: correction of sequence-based biases for accurate quantification of ribosome profiling data
title_full choros: correction of sequence-based biases for accurate quantification of ribosome profiling data
title_fullStr choros: correction of sequence-based biases for accurate quantification of ribosome profiling data
title_full_unstemmed choros: correction of sequence-based biases for accurate quantification of ribosome profiling data
title_short choros: correction of sequence-based biases for accurate quantification of ribosome profiling data
title_sort choros: correction of sequence-based biases for accurate quantification of ribosome profiling data
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9980091/
https://www.ncbi.nlm.nih.gov/pubmed/36865295
http://dx.doi.org/10.1101/2023.02.21.529452
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