Improved computational analysis of ribosome dynamics from 5'P degradome data using fivepeseq

Abstract

In eukaryotes, 5-3 co-translation degradation machinery follows the last translating ribosome providing an in vivo footprint of its position. Thus 5P degradome sequencing, in addition to informing about RNA decay, also provides valuable information regarding ribosome dynamics. Multiple experimental methods have been developed to investigate the mRNA degradome, however computational tools for their reproducible analysis are lacking. Here we present fivepseq: an easy-to-use application for analysis and interactive visualization of 5P degradome data. This tool performs both metagene and gene specific analysis, and allows to easily investigate codon specific ribosome pauses. To demonstrate its ability to provide new biological information, we investigate gene specific ribosome pauses in S. cerevisiae after eIF5A depletion. In addition to identifying pauses at expected codon motifs, we identify multiple genes with strain-specific frameshifts. To show its wide applicability, we investigate more complex 5P degradome from A. thaliana and discover both motif-specific ribosome protection associated with particular developmental stages, as well as generally increased ribosome protection at termination level associated with age. Our work shows how the use of improved analysis tools for the study of 5P degradome can significantly increase the biological information that can be derived from such datasets and facilitate its reproducible analysis. KEY POINTSO_LIAnalysis of 5P degradome data with fivepseq informs about global and gene-specific translational features. C_LIO_LIFrameshifts in translation-related genes in S. cerevisiae may be linked to ribosome stalling. C_LIO_LIRibosome protection at termination and codon motifs are linked to development in A. Thaliana. C_LI