Translation serves as an important layer of regulatory control, intricately influencing gene expression and protein functionality. Due to a phenomenon called, codon usage bias, highly expressed genes are believed to have codons that are translated more rapidly. As more than one codon can code for the same amino acid (synonymous codons), organisms may exhibit preferences for specific codons that facilitate increased expression of important genes and the translation speed of codons has been suggested to be linked to the availability of corresponding tRNAs. Furthermore, a new technique called ribosome profiling has recently permitted the study of the translatome, which refers to the entire population of mRNA associated with ribosomes for protein synthesis. This cutting-edge technique allows the identification of actively translated regions, but can also reveal translational pausing events that stem from the presence of SNPs. Interestingly, our previous research has demonstrated variation in tRNA expression across tissues and different states of health, leading us to consider the connection between tRNA abundance and translational stalling due to SNPs. By coupling ribosome profiling with tRNA sequencing and RNA sequencing, we can investigate all elements of translational machinery in order to predict translational efficiency, estimate proteome composition, and evaluate tRNA abundance as a source of genetic variation. In this work, we utilized ribosome profiling, tRNAseq, and RNAseq and perform an integrative analysis in bovine tissues (kidney, liver and muscle) as well as murine myoblast cell lines (C2C12). By applying these methods to different bovine tissues, we were able to explore the interplay between tRNA availability and translational stalling events as well as genes subject to modulation at transcriptional and translational levels that underlie tissue specific biological processes. Through the implementation of these next generation sequencing (NGS) methods to cell culture, we were able to evaluate the translatome at various time points (0-min, 30-min, 60-min, and 4-hour) post-induction of differentiation. Where most studies have focused on molecular changes between differentiating myoblasts and multinucleated myotubes that are present 7 days after differentiation, we focus on the earliest stages of muscle differentiation that initiate muscle development and therefore kickstart the process of meat production.
Anna K. Goldkamp (Fri,) studied this question.