Conserved non-AUG uORFs revealed by a novel regression analysis of ribosome profiling data

• Published in: Genome research Vol. 28; no. 2; pp. 214 - 222
• Main Authors: Spealman, Pieter, Naik, Armaghan W., May, Gemma E., Kuersten, Scott, Freeberg, Lindsay, Murphy, Robert F., McManus, Joel
• Format: Journal Article
• Language: English
• Published: United States Cold Spring Harbor Laboratory Press 01.02.2018
• Subjects: Codons; Conserved sequence; Gene expression; Growth conditions; Learning algorithms; mRNA turnover; Open reading frames; Saccharomyces; Species; Statistical analysis; Transcription initiation
• ISSN: 1088-9051; 1549-5469; 1549-5469
• DOI: 10.1101/gr.221507.117

Upstream open reading frames (uORFs), located in transcript leaders (5′ UTRs), are potent cis -acting regulators of translation and mRNA turnover. Recent genome-wide ribosome profiling studies suggest that thousands of uORFs initiate with non-AUG start codons. Although intriguing, these non-AUG uORF predictions have been made without statistical control or validation; thus, the importance of these elements remains to be demonstrated. To address this, we took a comparative genomics approach to study AUG and non-AUG uORFs. We mapped transcription leaders in multiple Saccharomyces yeast species and applied a novel machine learning algorithm (uORF-seqr) to ribosome profiling data to identify statistically significant uORFs. We found that AUG and non-AUG uORFs are both frequently found in Saccharomyces yeasts. Although most non-AUG uORFs are found in only one species, hundreds have either conserved sequence or position within Saccharomyces . uORFs initiating with UUG are particularly common and are shared between species at rates similar to that of AUG uORFs. However, non-AUG uORFs are translated less efficiently than AUG-uORFs and are less subject to removal via alternative transcription initiation under normal growth conditions. These results suggest that a subset of non-AUG uORFs may play important roles in regulating gene expression.