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Codon Usage and 3' UTR Length Determine Maternal mRNA Stability in Zebrafish.

Mol. Cell. 2016 Mar 17;61(6):874-85
Yuichiro Mishima 1 , Yukihide Tomari 2
Yuichiro Mishima 1 , Yukihide Tomari 2

[No authors listed]

Author information
  • 1 Institute 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. Electronic address: mishima@iam.u-tokyo.ac.jp.
  • 2 Institute 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.

摘要


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 with long conferring resistance to deadenylation. These results indicate that the combined effect of codon usage and 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.

原始数据


 保存测序数据
Sample name
Organism Experiment title Sample type Library instrument Attributes
source namestagesstraintissuetreatment
6hpf_amanitin
Danio rerio GSM1841189: 6hpf_amanitin; Danio rerio; RNA-Seq RNA-Seq Illumina HiSeq 2000 whole embryo 6 hpf AB whole embryo a-amanitin injected
6hpf_controlB
Danio rerio GSM1841188: 6hpf_controlB; Danio rerio; RNA-Seq RNA-Seq Illumina HiSeq 2000 whole embryo 6 hpf AB whole embryo control (for amanitin experiment)
6hpf_CNOT7DN
Danio rerio GSM1841187: 6hpf_CNOT7DN; Danio rerio; RNA-Seq RNA-Seq Illumina HiSeq 2000 whole embryo 6 hpf AB whole embryo CNOT7-DN injected
6hpf_430MO
Danio rerio GSM1841186: 6hpf_430MO; Danio rerio; RNA-Seq RNA-Seq Illumina HiSeq 2000 whole embryo 6 hpf AB whole embryo miR-430 MO injected
6hpf_control
Danio rerio GSM1841185: 6hpf_control; Danio rerio; RNA-Seq RNA-Seq Illumina HiSeq 2000 whole embryo 6 hpf AB whole embryo control