Codon Usage and 3' UTR Length Determine Maternal mRNA Stability in Zebrafish - PubMed (original) (raw)
Codon Usage and 3' UTR Length Determine Maternal mRNA Stability in Zebrafish
Yuichiro Mishima et al. Mol Cell. 2016.
Free article
Abstract
The control of mRNA stability plays a central role in regulating gene expression. In metazoans, the earliest stages of development are driven by maternally supplied mRNAs. The degradation of these maternal mRNAs is critical for promoting the maternal-to-zygotic transition of developmental programs, although the underlying mechanisms are poorly understood in vertebrates. Here, we characterized maternal mRNA degradation pathways in zebrafish using a transcriptome analysis and systematic reporter assays. Our data demonstrate that ORFs enriched with uncommon codons promote deadenylation by the CCR4-NOT complex in a translation-dependent manner. This codon-mediated mRNA decay is conditional on the context of the 3' UTR, with long 3' UTRs conferring resistance to deadenylation. These results indicate that the combined effect of codon usage and 3' UTR length determines the stability of maternal mRNAs in zebrafish embryos. Our study thus highlights the codon-mediated mRNA decay as a conserved regulatory mechanism in eukaryotes.
Copyright © 2016 Elsevier Inc. All rights reserved.
Comment in
- A Universal Code for mRNA Stability?
Chen YH, Coller J. Chen YH, et al. Trends Genet. 2016 Nov;32(11):687-688. doi: 10.1016/j.tig.2016.08.007. Epub 2016 Sep 1. Trends Genet. 2016. PMID: 27594172 Free PMC article. Review.
Similar articles
- A Universal Code for mRNA Stability?
Chen YH, Coller J. Chen YH, et al. Trends Genet. 2016 Nov;32(11):687-688. doi: 10.1016/j.tig.2016.08.007. Epub 2016 Sep 1. Trends Genet. 2016. PMID: 27594172 Free PMC article. Review. - A Massively Parallel Reporter Assay of 3' UTR Sequences Identifies In Vivo Rules for mRNA Degradation.
Rabani M, Pieper L, Chew GL, Schier AF. Rabani M, et al. Mol Cell. 2017 Dec 21;68(6):1083-1094.e5. doi: 10.1016/j.molcel.2017.11.014. Epub 2017 Dec 7. Mol Cell. 2017. PMID: 29225039 Free PMC article. - Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition.
Bazzini AA, Del Viso F, Moreno-Mateos MA, Johnstone TG, Vejnar CE, Qin Y, Yao J, Khokha MK, Giraldez AJ. Bazzini AA, et al. EMBO J. 2016 Oct 4;35(19):2087-2103. doi: 10.15252/embj.201694699. Epub 2016 Jul 19. EMBO J. 2016. PMID: 27436874 Free PMC article. - RNA tales - how embryos read and discard messages from mom.
Despic V, Neugebauer KM. Despic V, et al. J Cell Sci. 2018 Mar 1;131(5):jcs201996. doi: 10.1242/jcs.201996. J Cell Sci. 2018. PMID: 29467249 Review. - Mature maternal mRNAs are longer than zygotic ones and have complex degradation kinetics in sea urchin.
Gildor T, Malik A, Sher N, Ben-Tabou de-Leon S. Gildor T, et al. Dev Biol. 2016 Jun 1;414(1):121-31. doi: 10.1016/j.ydbio.2016.04.007. Epub 2016 Apr 13. Dev Biol. 2016. PMID: 27085752
Cited by
- A nascent peptide code for translational control of mRNA stability in human cells.
Burke PC, Park H, Subramaniam AR. Burke PC, et al. Nat Commun. 2022 Nov 11;13(1):6829. doi: 10.1038/s41467-022-34664-0. Nat Commun. 2022. PMID: 36369503 Free PMC article. - Eukaryotic mRNA decapping factors: molecular mechanisms and activity.
He F, Jacobson A. He F, et al. FEBS J. 2023 Nov;290(21):5057-5085. doi: 10.1111/febs.16626. Epub 2022 Sep 30. FEBS J. 2023. PMID: 36098474 Free PMC article. Review. - Plant 3' Regulatory Regions From mRNA-Encoding Genes and Their Uses to Modulate Expression.
Bernardes WS, Menossi M. Bernardes WS, et al. Front Plant Sci. 2020 Aug 14;11:1252. doi: 10.3389/fpls.2020.01252. eCollection 2020. Front Plant Sci. 2020. PMID: 32922424 Free PMC article. Review. - Relationship between circulating thrombospondin-1 messenger ribonucleic acid and microribonucleic acid-194 levels in Chinese patients with type 2 diabetic kidney disease: The outcomes of a case-control study.
Ma N, Liu W, Xu N, Yin D, Zheng P, Wang G, Hui Y, Zhang J, Han G, Yang C, Lu Y, Cheng X. Ma N, et al. J Diabetes Investig. 2024 Sep;15(9):1248-1258. doi: 10.1111/jdi.14252. Epub 2024 Jun 26. J Diabetes Investig. 2024. PMID: 38932465 Free PMC article. - The organization and regulation of mRNA-protein complexes.
Rissland OS. Rissland OS. Wiley Interdiscip Rev RNA. 2017 Jan;8(1):e1369. doi: 10.1002/wrna.1369. Epub 2016 Jun 21. Wiley Interdiscip Rev RNA. 2017. PMID: 27324829 Free PMC article. Review.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources
Molecular Biology Databases