UMMS Affiliation

Department of Microbiology and Physiological Systems; Graduate School of Biomedical Sciences

Publication Date


Document Type



Biochemistry, Biophysics, and Structural Biology | Cellular and Molecular Physiology | Genetics and Genomics


Translation of mRNA into a polypeptide is terminated when the release factor eRF1 recognizes a UAA, UAG, or UGA stop codon in the ribosomal A site and stimulates nascent peptide release. However, “stop codon readthrough” can occur when a near-cognate tRNA outcompetes eRF1 in decoding the stop codon, resulting in the continuation of elongation into the mRNA 3’-UTR. Previous studies with reporter systems have shown that the efficiency of termination or readthrough is modulated by cis-acting elements other than stop codon identity, including two nucleotides 5’ of the stop codon, six nucleotides 3’ of the stop codon in the ribosomal mRNA channel, and stem-loop structures in the mRNA 3’-UTR. It remains to be determined whether these elements are important at a genome-wide level and whether other mRNA features proximal to the stop codon significantly affect termination and readthrough efficiencies in vivo. Accordingly, we carried out ribosome profiling analyses of yeast cells expressing wild-type or temperature-sensitive eRF1 and developed bioinformatics strategies to calculate readthrough efficiency, and to identify mRNA and peptide features which influence that efficiency. Our analyses revealed that the most influential features consist of the stop codon (nt +1 to +3), the nucleotide after it (nt +4), the codon in the P site (nt -3 to -1), and 3’-UTR length, while nts +5 to +9 and mRNA secondary structure in the 3’-UTR had milder effects. Additionally, we found low readthrough genes to have shorter 3’-UTRs compared to high readthrough genes in cells with thermally inactivated eRF1, while this trend was reversed in wild-type cells. Together, our results confirmed the general roles of known regulatory elements in genome-wide regulation and identified several new mRNA or peptide features important for translation termination and readthrough.


mRNA, stop codon, translation, termination, readthrough

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Copyright © 2020 The Author(s). This is an open access document distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

DOI of Published Version


Journal/Book/Conference Title

25th Annual University of Massachusetts Medical School Research Retreat 2020


Poster presented virtually at the 25th Annual University of Massachusetts Medical School Research Retreat 2020 on October 26, 2020.

Creative Commons License

Creative Commons Attribution 4.0 License
This work is licensed under a Creative Commons Attribution 4.0 License.



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