RiboPlotR: a visualization tool for periodic Ribo-seq reads.

Area of Science:

• Molecular Biology
• Genomics
• Bioinformatics

Background:

• Ribosome profiling (Ribo-seq) is a powerful technique for studying genome-wide mRNA translation.
• High-quality Ribo-seq data exhibit a distinct 3-nucleotide periodicity, reflecting ribosome movement.
• Existing tools for visualizing Ribo-seq data and associated novel translation events are underdeveloped.

Purpose of the Study:

• To develop a visualization tool for Ribo-seq data.
• To facilitate the identification and study of novel translation events, including upstream open reading frames (uORFs) and small open reading frames (sORFs).
• To improve the understanding of translation regulation mechanisms.

Main Methods:

• Developed RiboPlotR, an R package for data visualization.
• RiboPlotR integrates RNA-seq coverage and Ribo-seq reads in genomic coordinates.
• The package visualizes data for all annotated transcript isoforms, including UTRs and introns, with color-coded reading frames.

Main Results:

• RiboPlotR effectively visualizes Ribo-seq data alongside gene structures.
• The tool facilitates the observation of novel translation events by presenting reads across three reading frames.
• Visualization aids in identifying potential regulatory mechanisms influencing translation.

Conclusions:

• RiboPlotR is a freely available visualization package for Ribo-seq data.
• The tool enhances the exploration of translated features identified through Ribo-seq.
• RiboPlotR supports the discovery and characterization of complex translation events.