5PSeq Explorer: interactive analysis of co-translational mRNA decay and ribosome dynamics

Area of Science:

• Molecular Biology
• Bioinformatics
• Genomics

Background:

• Co-translational mRNA decay involves 5' to 3' exonucleases following translating ribosomes.
• This process generates 5' ribosome protected fragments (5PSeq), offering insights into ribosome dynamics.
• Systematic analysis resources for 5PSeq intermediates and associated features like ribosome stalls are limited.

Purpose of the Study:

• To develop a comprehensive platform for analyzing 5PSeq data.
• To enable in-depth exploration of ribosome dynamics in vivo.
• To facilitate the study of the interplay between mRNA decay and ribosome behavior.

Main Methods:

• Developed 5PSeq Explorer, a web-based platform.
• Utilized 773 uniformly processed 5PSeq datasets from 23 species (bacteria and Ascomycota).
• Integrated normalized counts, structured metadata, and scalable visualization tools.

Main Results:

• 5PSeq Explorer allows exploration of ribosome dynamics at codon, amino acid, and transcript levels.
• The platform provides a framework for studying the crosstalk between mRNA decay and ribosome dynamics.
• Offers both a public web interface and a Docker-based local version for accessibility and reproducibility.

Conclusions:

• 5PSeq Explorer enhances the systematic analysis of ribosome dynamics using 5PSeq data.
• The platform supports research into mRNA decay mechanisms and ribosome behavior.
• Provides a valuable, accessible resource for the scientific community.