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STATR: A simple analysis pipeline of Ribo-Seq in bacteria

Gene expression changes in response to diverse environmental stimuli to regulate numerous cellular functions. Genes are expressed into their functional products with the help of messenger RNA (mRNA). Thus, measuring levels of mRNA in cells is important to understand cellular functions. With advances...

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Autores principales: Choe, Donghui, Palsson, Bernhard, Cho, Byung-Kwan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7209825/
https://www.ncbi.nlm.nih.gov/pubmed/31989542
http://dx.doi.org/10.1007/s12275-020-9536-2
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author Choe, Donghui
Palsson, Bernhard
Cho, Byung-Kwan
author_facet Choe, Donghui
Palsson, Bernhard
Cho, Byung-Kwan
author_sort Choe, Donghui
collection PubMed
description Gene expression changes in response to diverse environmental stimuli to regulate numerous cellular functions. Genes are expressed into their functional products with the help of messenger RNA (mRNA). Thus, measuring levels of mRNA in cells is important to understand cellular functions. With advances in next-generation sequencing (NGS), the abundance of cellular mRNA has been elucidated via transcriptome sequencing. However, several studies have found a discrepancy between mRNA abundance and protein levels induced by translational regulation, including different rates of ribosome entry and translational pausing. As such, the levels of mRNA are not necessarily a direct representation of the protein levels found in a cell. To determine a more precise way to measure protein expression in cells, the analysis of the levels of mRNA associated with ribosomes is being adopted. With an aid of NGS techniques, a single nucleotide resolution footprint of the ribosome was determined using a method known as Ribo-Seq or ribosome profiling. This method allows for the high-throughput measurement of translation in vivo, which was further analyzed to determine the protein synthesis rate, translational pausing, and cellular responses toward a variety of environmental changes. Here, we describe a simple analysis pipeline for Ribo-Seq in bacteria, so-called simple translatome analysis tool for Ribo-Seq (STATR). STATR can be used to carry out the primary processing of Ribo-Seq data, subsequently allowing for multiple levels of translatome study, from experimental validation to in-depth analyses. A command-by-command explanation is provided here to allow a broad spectrum of biologists to easily reproduce the analysis.
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spelling pubmed-72098252021-03-01 STATR: A simple analysis pipeline of Ribo-Seq in bacteria Choe, Donghui Palsson, Bernhard Cho, Byung-Kwan J Microbiol Article Gene expression changes in response to diverse environmental stimuli to regulate numerous cellular functions. Genes are expressed into their functional products with the help of messenger RNA (mRNA). Thus, measuring levels of mRNA in cells is important to understand cellular functions. With advances in next-generation sequencing (NGS), the abundance of cellular mRNA has been elucidated via transcriptome sequencing. However, several studies have found a discrepancy between mRNA abundance and protein levels induced by translational regulation, including different rates of ribosome entry and translational pausing. As such, the levels of mRNA are not necessarily a direct representation of the protein levels found in a cell. To determine a more precise way to measure protein expression in cells, the analysis of the levels of mRNA associated with ribosomes is being adopted. With an aid of NGS techniques, a single nucleotide resolution footprint of the ribosome was determined using a method known as Ribo-Seq or ribosome profiling. This method allows for the high-throughput measurement of translation in vivo, which was further analyzed to determine the protein synthesis rate, translational pausing, and cellular responses toward a variety of environmental changes. Here, we describe a simple analysis pipeline for Ribo-Seq in bacteria, so-called simple translatome analysis tool for Ribo-Seq (STATR). STATR can be used to carry out the primary processing of Ribo-Seq data, subsequently allowing for multiple levels of translatome study, from experimental validation to in-depth analyses. A command-by-command explanation is provided here to allow a broad spectrum of biologists to easily reproduce the analysis. 2020-01-28 2020-03 /pmc/articles/PMC7209825/ /pubmed/31989542 http://dx.doi.org/10.1007/s12275-020-9536-2 Text en http://creativecommons.org/licenses/by/4.0 may be reused by Creative Commons Attribution 4.0 International License.
spellingShingle Article
Choe, Donghui
Palsson, Bernhard
Cho, Byung-Kwan
STATR: A simple analysis pipeline of Ribo-Seq in bacteria
title STATR: A simple analysis pipeline of Ribo-Seq in bacteria
title_full STATR: A simple analysis pipeline of Ribo-Seq in bacteria
title_fullStr STATR: A simple analysis pipeline of Ribo-Seq in bacteria
title_full_unstemmed STATR: A simple analysis pipeline of Ribo-Seq in bacteria
title_short STATR: A simple analysis pipeline of Ribo-Seq in bacteria
title_sort statr: a simple analysis pipeline of ribo-seq in bacteria
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7209825/
https://www.ncbi.nlm.nih.gov/pubmed/31989542
http://dx.doi.org/10.1007/s12275-020-9536-2
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