Errors and the evolution of genomes : the role of stop codons

• Main Author: Abrahams, Liam
• Format: Dissertation
• Language: English
• Published: University of Bath 2020

The multi-step process of converting information stored in DNA to functional molecules is inherently error-prone. As we move towards an era of precision medicine, understanding why such errors occur is essential both for accurate diagnosis and therapeutic design. However, also interesting is how genomes have evolved to prevent or mitigate the deleterious consequences of such errors. In this thesis, I use stop codons as an exemplar, as their presence/absence in sequence outside of translation termination may be indicative of function. I ask two broader questions: first, are vital components that ensure accurate splicing, exonic splice enhancers (ESEs), constrained by often residing in coding sequence? If so, do these constraints apply to other sequences? I show stop codons are depleted in ESEs and this depletion is most parsimonious with functioning in CDS. Consequently, stop codons in long intergenic noncoding RNAs (lincRNAs) are also unexpectedly depleted, attributable to the presence of ESEs. This depletion appears to result in a susceptibility to nonsense mutational errors, resulting in nonsense-associated altered splicing (NAS). I find ~6% of genome-wide nonsense mutations in healthy individuals result in exon skipping, but such an effect is probably stronger when disease-associated. Given ESE use in the human genome, I turned my attention to bacterial genomes to ask a second question: are stop codons employed as a direct error-proofing mechanism? I find bacterial genomes appear select for out of frame stop codons to terminate frameshifts based on their probability of frameshifting, and not downstream costs. Interestingly, I also show that in bacterial genes, a stop codon appears to be selected for immediately following the start codon, hypothesising that this helps the ribosome correctly initiate translation initiation. Stop codons are therefore implicated genome-wide in both preventing errors and making genes more susceptible to errors.