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

Area of Science:

• Molecular Biology
• Genomics
• Bioinformatics

Background:

• Gene expression regulation is crucial for cellular functions.
• Messenger RNA (mRNA) levels are commonly measured, but may not directly correlate with protein levels due to translational control.
• Ribosome profiling (Ribo-Seq) provides a more accurate measure of protein synthesis by analyzing mRNA associated with ribosomes.

Purpose of the Study:

• To present a straightforward analysis pipeline for Ribo-Seq data in bacteria.
• To enable researchers to perform detailed translatome studies.
• To facilitate the understanding of cellular responses to environmental changes at the translational level.

Main Methods:

• Utilized next-generation sequencing (NGS) techniques for Ribo-Seq.
• Developed a simple translatome analysis tool for Ribo-Seq (STATR) for primary data processing.
• Provided a command-by-command guide for reproducible analysis.

Main Results:

• STATR enables high-throughput measurement of translation in vivo.
• The pipeline facilitates the analysis of protein synthesis rates and translational pausing.
• The tool supports in-depth translatome studies and experimental validation.

Conclusions:

• STATR simplifies the analysis of Ribo-Seq data in bacteria.
• This tool empowers biologists to conduct comprehensive translational studies.
• Accurate measurement of protein synthesis is essential for understanding cellular dynamics.