BLT Stages

Abstract 2018-2019: Translation efficiency regulation by mapping ribosome profiling data to coding sequences and 5’UTRs 

The five prime untranslated region (5’UTR) region of mRNA and, in particular, the regulatory effect it has on translational regulation is a largely unstudied subject. Some papers suggest that there is translation regulation of the coding sequence (CDS) by accumulating ribosomes in the 5’UTR end of the mRNA, reducing ribosomes in the CDS. However, this has never been examined closely. Therefore, this project focusses on the 5’UTR domain and the upstream ORFs (uORFs) therein using ribosome profiling data. Ribosome profiling is a relative new technique that uses sequencing data from ribosome protected mRNA fragments. A huge advantage of this technique over RNA sequencing is that in most datasets, a 3-nucleotide periodicity can be seen indicating where the mRNA is being translated. This allows looking at the sites where translation is occurring in CDS and the 5’UTR region. In this project, the ratio of the number of reads in the 5’UTR region versus the number of reads in the corresponding CDS is examined showing that in most cases there is an increase in this ratio in stress versus normal condition. Besides this, the uORFs in the 5’UTR are also examined using a tool called ribORF to see if any of them show a sign of being translated. According to the results of ribORF there is a significant translation in uORFs in most datasets allowing differential expression analyses on these uORFs and comparing them with their corresponding CDS. The dataset with the highest coverages shows that the changes in uORF and CDS on the same transcript tend to be concordant.