- STATR: A simple analysis pipeline of Ribo-Seq in bacteria
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Donghui Choe , Bernhard Palsson , Byung-Kwan Cho
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J. Microbiol. 2020;58(3):217-226. Published online January 28, 2020
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DOI: https://doi.org/10.1007/s12275-020-9536-2
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 Abstract
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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 highthroughput
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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Citations
Citations to this article as recorded by  - Translation in Bacillus subtilis is spatially and temporally coordinated during sporulation
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Journal of Microbiology.2020; 58(3): 173. CrossRef
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