Header

UZH-Logo

Maintenance Infos

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


Castelo-Szekely, Violeta; De Matos, Mara; Tusup, Marina; Pascolo, Steve; Ule, Jernej; Gatfield, David (2019). Charting DENR-dependent translation reinitiation uncovers predictive uORF features and links to circadian timekeeping via Clock. Nucleic Acids Research, 47(10):5193-5209.

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.

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.

Statistics

Citations

Dimensions.ai Metrics
2 citations in Web of Science®
1 citation in Scopus®
Google Scholar™

Altmetrics

Downloads

22 downloads since deposited on 21 Aug 2019
22 downloads since 12 months
Detailed statistics

Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:04 Faculty of Medicine > University Hospital Zurich > Dermatology Clinic
Dewey Decimal Classification:610 Medicine & health
Uncontrolled Keywords:Genetics
Language:English
Date:4 June 2019
Deposited On:21 Aug 2019 14:29
Last Modified:25 Sep 2019 00:42
Publisher:Oxford University Press
ISSN:0305-1048
OA Status:Gold
Publisher DOI:https://doi.org/10.1093/nar/gkz261
Project Information:
  • : FunderSNSF
  • : Grant IDPP00P3_157528
  • : Project TitleTranslational control within the circadian clock
  • : FunderSNSF
  • : Grant ID31003A_179190
  • : Project TitleMolecular mechanisms and physiological signals underlying daily rhythms in translation

Download

Gold Open Access

Download PDF  'Charting DENR-dependent translation reinitiation uncovers predictive uORF features and links to circadian timekeeping via Clock'.
Preview
Content: Published Version
Filetype: PDF
Size: 4MB
View at publisher
Licence: Creative Commons: Attribution 4.0 International (CC BY 4.0)