Charting DENR-dependent translation reinitiation uncovers predictive uORF features and links to circadian timekeeping via Clock.

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Version: Final published version
License: CC BY 4.0
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Version: Supplementary document
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Serval ID
serval:BIB_9D401C4DBF9B
Type
Article: article from journal or magazin.
Collection
Publications
Title
Charting DENR-dependent translation reinitiation uncovers predictive uORF features and links to circadian timekeeping via Clock.
Journal
Nucleic acids research
Author(s)
Castelo-Szekely V., De Matos M., Tusup M., Pascolo S., Ule J., Gatfield D.
ISSN
1362-4962 (Electronic)
ISSN-L
0305-1048
Publication state
Published
Issued date
04/06/2019
Peer-reviewed
Oui
Volume
47
Number
10
Pages
5193-5209
Language
english
Notes
Publication types: Journal Article ; Research Support, Non-U.S. Gov't
Publication Status: ppublish
Abstract
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.
Keywords
5' Untranslated Regions, Animals, CLOCK Proteins/genetics, CLOCK Proteins/metabolism, Circadian Rhythm, Cloning, Molecular, Codon, Initiator, Eukaryotic Initiation Factors/genetics, Eukaryotic Initiation Factors/metabolism, Fibroblasts/metabolism, Gene Expression Regulation, HEK293 Cells, Humans, Luciferases/metabolism, Mice, Mutation, NIH 3T3 Cells, Open Reading Frames, RNA, Messenger/metabolism, Ribosomes/metabolism
Pubmed
Web of science
Open Access
Yes
Funding(s)
Swiss National Science Foundation / Careers / PP00P3_157528
Swiss National Science Foundation / Projects / 31003A_179190
University of Lausanne
Create date
11/06/2019 12:37
Last modification date
16/12/2019 7:19
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