RT Journal Article
SR Electronic
T1 Unraveling the influences of sequence and position on yeast uORF activity using massively parallel reporter systems and machine learning
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.04.16.440232
DO 10.1101/2021.04.16.440232
A1 Gemma May
A1 Christina Akirtava
A1 Matthew Agar-Johnson
A1 Jelena Micic
A1 John Woolford
A1 Joel McManus
YR 2021
UL http://biorxiv.org/content/early/2021/04/17/2021.04.16.440232.abstract
AB Upstream open reading frames (uORFs) are potent cis-acting regulators of mRNA translation and nonsense-mediated decay (NMD). While both AUG- and non-AUG initiated uORFs are ubiquitous in ribosome profiling studies, few uORFs have been experimentally tested. Consequently, the relative influences of sequence, structural, and positional features on uORF activity have not been determined. We quantified thousands of yeast uORFs using massively parallel reporter assays in wildtype and Δupf1 yeast. While nearly all AUG uORFs were robust repressors, most non-AUG uORFs had relatively weak impacts on expression. Machine learning regression modeling revealed that uORF functions are strongly impacted by both their sequences and locations within transcript leaders. Indeed, alternative transcription start sites highly influenced uORF activity. These results define the scope of natural uORF activity, identify features associated with translational repression and NMD, and suggest that the locations of uORFs in transcript leaders are nearly as important as uORF sequences.Competing Interest StatementThe authors have declared no competing interest.