Bioinformatical analysis of RNAse preference for specific nuclotides in Ribosome Profiling data

Ribosome Profiling (RP) is a methodology for assessing the translation dynamics, specifically the amount of ribosomes found on each position of a given transcript. It can be extended to assess the rate of translation, allowing to infer which mRNA sequences can lead to easier translation, ribosome collisions, and defects in translation. RP is done by the RNA sequencing of mRNA regions covered by the ribosomes, followed by its mapping to the genome. One of the key limitations of the RP procedure is its resolution: the inference of the exact codon being translated by the A-site of the ribosome can be imprecise, since the length of the mRNA covered by the ribosome can vary, usually from 27 to 32 nucleotides, which demands bioinformatics tools for its inference. One of the aspects that leads to this variation is the lysis preference for specific nucleotides by RNAse I, used for degradation of the regions of mRNA not covered by the ribosome. Currently, the mainly used bioinformatics tools ignore nucleotide context to predict the ribosome position in the transcript, relying only on the length of the mRNA stretch protected by the ribosome.

Our group is developing a new bioinformatics tool to assess these nucleotide preferences. Our tool is capable of considering not only the mRNA stretch length, but also the patterns of the nucleotides on its ends and around it, allowing for better precision in ribosome position inferring, with nucleotide resolution. Our data show that, by considering the nucleotide patterns around the RP stretches, the precision of the Ribosome Profiling processing can be improved, allowing for already existing data to be used for analyzing transcripts with low expression that would be otherwise inaccessible to the currently used methodologies.

This work was supported by Conselho Nacional de Desesenvolvimento Científico e Tecnologico (CNPq), by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) and by the Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ).