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Genome Biol January 5, 2021; 22 (1): 14.

Crosstalk between codon optimality and cis-regulatory elements dictates mRNA stability.

Medina-Muñoz SG , Kushawah G , Castellano LA , Diez M , DeVore ML , Salazar MJB , Bazzini AA .

BACKGROUND: The regulation of messenger RNA (mRNA) stability has a profound impact on gene expression dynamics during embryogenesis. For example, in animals, maternally deposited mRNAs are degraded after fertilization to enable new developmental trajectories. Regulatory sequences in 3'' untranslated regions (3''UTRs) have long been considered the central determinants of mRNA stability. However, recent work indicates that the coding sequence also possesses regulatory information. Specifically, translation in cis impacts mRNA stability in a codon-dependent manner. However, the strength of this mechanism during embryogenesis, as well as its relationship with other known regulatory elements, such as microRNA, remains unclear. RESULTS: Here, we show that codon composition is a major predictor of mRNA stability in the early embryo. We show that this mechanism works in combination with other cis-regulatory elements to dictate mRNA stability in zebrafish and Xenopus embryos as well as in mouse and human cells. Furthermore, we show that microRNA targeting efficacy can be affected by substantial enrichment of optimal (stabilizing) or non-optimal (destabilizing) codons. Lastly, we find that one microRNA, miR-430, antagonizes the stabilizing effect of optimal codons during early embryogenesis in zebrafish. CONCLUSIONS: By integrating the contributions of different regulatory mechanisms, our work provides a framework for understanding how combinatorial control of mRNA stability shapes the gene expression landscape.

PubMed ID: 33402205
PMC ID: PMC7783504
Article link: Genome Biol
Grant support: [+]

Species referenced: Xenopus laevis
Genes referenced: dicer1
GO keywords: regulation of mRNA stability

Article Images: [+] show captions
References [+] :
Aanes, Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition. 2012, Pubmed