rnaends: an R package to study exact RNA ends at nucleotide resolution

Abstract

AO_SCPLOWBSTRACTC_SCPLOW5 and 3 RNA-end sequencing protocols have unlocked new opportunities to study aspects of RNA metabolism such as synthesis, maturation and degradation, by enabling the quantification of exact ends of RNA molecules in vivo. From RNA-Seq data that have been generated with one of the specialized protocols, it is possible to identify transcription start sites (TSS) and/or endoribonucleolytic cleavage sites, and even, in some cases, co-translational 5 to 3 degradation dynamics. Furthermore, post-transcriptional addition of ribonucleotides at the 3 end of RNA can be studied at the nucleotide resolution. While different RNA-end sequencing library protocols exist that have been adapted to a specific organism (prokaryote or eukaryote) or specific biological question, the generated RNA-Seq data are very similar and share common processing steps. Most importantly, the major aspect of RNA-end sequencing is that only the 5 or 3 end mapped location is of interest, contrary to conventional RNA sequencing that considers genomic ranges for gene expression analysis. This translates to a simple representation of the quantitative data as a count matrix of RNA-end location on the reference sequences. This representation seems under-exploited and is, to our knowledge, not available in a generic package focused on the analyses on the exact transcriptome ends. Here, we present the rnaends R package which is dedicated to RNA-end sequencing analysis. It offers functions for raw read pre-processing, RNA-end mapping and quantification, RNA-end count matrix post-processing, and further downstream count matrix analyses such as TSS identification, fast Fourier transform for signal periodic pattern analysis, or differential proportion of RNA-end analysis. The use of rnaends is illustrated here with applications in RNA metabolism studies through selected rnaends workflows on published RNA-end datasets: (i) TSS identification, (ii) ribosome translation speed and co-translational degradation, (iii) post-transcriptional modification analysis and differential proportion analysis.