Abstract
BackgroundRibo-seq has revolutionized the study of genome-wide mRNA translation. High-quality Ribo-seq data display strong 3-nucleotide (nt) periodicity, which corresponds to translating ribosomes deciphering three nts at a time. While 3-nt periodicity has been widely used to study novel translation events such as upstream ORFs in 5′ untranslated regions and small ORFs in presumed non-coding RNAs, tools that allow the visualization of these events remain underdeveloped.ResultsRiboPlotR is a visualization package written in R that presents both RNA-seq coverage and Ribo-seq reads in genomic coordinates for all annotated transcript isoforms of a gene. Specifically, for individual isoform models, RiboPlotR plots Ribo-seq data in the context of gene structures, including 5′ and 3′ untranslated regions and introns, and it presents the reads for all three reading frames in three different colors. The inclusion of gene structures and color-coding the reading frames facilitate observing new translation events and identifying potential regulatory mechanisms.ConclusionsRiboPlotR is freely available (https://github.com/hsinyenwu/RiboPlotR and https://sourceforge.net/projects/riboplotr/) and allows the visualization of translated features identified in Ribo-seq data.
Highlights
Ribo-seq has revolutionized the study of genome-wide mRNA translation
The Ribo-seq reads for each of the three reading frames are shown (Fig. 1A). This “single-transcript” style of plotting is useful for identifying overlapping translation events within a specific mature isoform but would miss Ribo-seq reads that belong to other isoforms, as well as those mapped to introns and unannotated coding exons
We describe the RiboPlotR package (Fig. 1B) for visualizing RNA-seq/Ribo-seq reads in the context of gene structures, including Ribo-seq reads mapped to the annotated coding sequences (CDSs), 5′ and 3′ untranslated regions (UTRs), and introns, with all annotated transcript isoform models displayed in parallel in the plot
Summary
RiboPlotR is a visualization package written in R that presents both RNA-seq coverage and Ribo-seq reads in genomic coordinates for all annotated transcript isoforms of a gene. For individual isoform models, RiboPlotR plots Ribo-seq data in the context of gene structures, including 5′ and 3′ untranslated regions and introns, and it presents the reads for all three reading frames in three different colors. The inclusion of gene structures and color-cod‐ ing the reading frames facilitate observing new translation events and identifying potential regulatory mechanisms
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