Charting DENR-dependent translation reinitiation uncovers predictive uORF features and links to circadian timekeeping via Clock
More about Open Access at the CrickAuthors list
Violeta Castelo-Szekely Mara De Matos Marina Tusup Steve Pascolo Jernej Ule David GatfieldAbstract
The non-canonical initiation factor DENR promotes translation reinitiation on mRNAs harbouring upstream open reading frames (uORFs). Moreover, DENR depletion shortens circadian period in mouse fibroblasts, suggesting involvement of uORF usage and reinitiation in clock regulation. To identify DENR-regulated translation events transcriptome-wide and, in particular, specific core clock transcripts affected by this mechanism, we have used ribosome profiling in DENR-deficient NIH3T3 cells. We uncovered 240 transcripts with altered translation rate, and used linear regression analysis to extract 5' UTR features predictive of DENR dependence. Among core clock genes, we identified Clock as a DENR target. Using Clock 5' UTR mutants, we mapped the specific uORF through which DENR acts to regulate CLOCK protein biosynthesis. Notably, these experiments revealed an alternative downstream start codon, likely representing the bona fide CLOCK N-terminus. Our findings provide insights into uORF-mediated translational regulation that can regulate the mammalian circadian clock and gene expression at large.
Journal details
Journal
Nucleic Acids Research
Volume
47
Issue number
10
Pages
5193-5209
Available online
Publication date
Full text links
Publisher website (DOI)
10.1093/nar/gkz261
Figshare
View on figshare
Europe PubMed Central
30982898
Pubmed
30982898
Keywords
Related topics
Type of publication
