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Series GSE71609 Query DataSets for GSE71609
Status Public on Mar 17, 2016
Title Codon usage and 3′ UTR length determine maternal mRNA stability in zebrafish
Organism Danio rerio
Experiment type Expression profiling by high throughput sequencing
Summary 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.
 
Overall design zebrafish embryonic mRNA profile at 2 different stages (2 hpf and 6 hpf) in wildtype and 3 additional conditions (miR-430 inhibition, RNApol II inhibition and CNOT7 inhibition) at 6 hpf. All experiments are performed as triplicates
 
Contributor(s) Mishima Y
Citation(s) 26990990
Submission date Jul 31, 2015
Last update date May 15, 2019
Contact name Yuichiro Mishima
E-mail(s) mishima@cc.kyoto-su.ac.jp
Phone +81-75-705-1943
Organization name Kyoto Sangyo University
Department Department of Frontier Life Sciences
Lab Mishima Lab
Street address Motoyama, Kamigamo,
City Kita-ku
State/province Kyoto
ZIP/Postal code 603-8555
Country Japan
 
Platforms (1)
GPL14875 Illumina HiSeq 2000 (Danio rerio)
Samples (6)
GSM1841184 2hpf_control
GSM1841185 6hpf_control
GSM1841186 6hpf_430MO
Relations
BioProject PRJNA291613
SRA SRP061886

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE71609_2015_MZT.txt.gz 2.9 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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