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Updated: Mar 24, 2026

Generation of Maternal Mutants Using zpc:cas9 Knock-in Zebrafish
Published on: July 22, 2025
Codon Usage and 3' UTR Length Determine Maternal mRNA Stability in Zebrafish
Yuichiro Mishima1, Yukihide Tomari1
1Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
Maternal mRNA degradation in zebrafish is controlled by uncommon codons, promoting deadenylation. This process is influenced by 3' untranslated region length, revealing a conserved mRNA decay mechanism.
Area of Science:
- Developmental Biology
- Molecular Biology
- Genetics
Background:
- mRNA stability is crucial for gene expression regulation.
- Maternal mRNAs fuel early development in metazoans.
- Mechanisms controlling maternal mRNA degradation in vertebrates are not well understood.
Purpose of the Study:
- To investigate maternal mRNA degradation pathways in zebrafish.
- To identify factors influencing maternal mRNA stability during early development.
Main Methods:
- Transcriptome analysis in zebrafish embryos.
- Systematic reporter assays to study mRNA decay.
- Analysis of codon usage and 3' untranslated region (UTR) effects.
Main Results:
- Open reading frames (ORFs) with uncommon codons enhance deadenylation via the CCR4-NOT complex in a translation-dependent manner.
- Long 3' UTRs confer resistance to this codon-mediated mRNA decay.
- Codon usage and 3' UTR length collectively determine maternal mRNA stability in zebrafish.
Conclusions:
- Codon-mediated mRNA decay is a significant regulatory mechanism for maternal mRNAs in zebrafish.
- This mechanism is conserved across eukaryotes, impacting developmental transitions.
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