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GEO Series: GSE52809

Title: Poly(A)-tail profiling reveals an embryonic switch in translational control

Summary

Poly(A) tails enhance the stability and translation of most eukaryotic messenger RNAs, but difficulties in globally measuring poly(A)-tail lengths have impeded greater understanding of poly(A)-tail function. Here we describe poly(A)-tail length profiling by sequencing (PAL-seq) and apply it to measure tail lengths of millions of individual RNAs isolated from yeasts, cell lines, Arabidopsis thaliana leaves, mouse liver, and zebrafish and frog embryos. Poly(A)-tail lengths were conserved between orthologous mRNAs, with mRNAs encoding ribosomal proteins and other 'housekeeping' proteins tending to have shorter tails. As expected, tail lengths were coupled to translational efficiencies in early zebrafish and frog embryos. However, this strong coupling diminished at gastrulation and was absent in non-embryonic samples, indicating a rapid developmental switch in the nature of translational control. This switch complements an earlier switch to zygotic transcriptional control and explains why the predominant effect of microRNA mediated deadenylation concurrently shifts from translational repression to mRNA destabilization.


Contributors: Stephen Eichhorn, Alexander Subtelny, Stephen Eichhorn, Grace Chen, Hazel Sive, David Bartel

Experiment Type: 64 samples from a variety of species

Article: Xenbase, PubMed

Source: NCBI GEO, Xenbase FTP

Samples: (DEG = Differentially Expressed Genes; GSM = GEO Sample Number)
Sample View GSMs Assay Type
WE - NF12-12.5 GSM1316825  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 12 to NF stage 12.5  
WE - NF12-12.5 (PAL-Seq) GSM1316827  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 12 to NF stage 12.5  
WE - NF12-12.5 (Ribo-Seq) GSM1316826  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 12 to NF stage 12.5  
WE - NF3-4 GSM1276563  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 3 (4-cell) to NF stage 4 (8-cell)  
WE - NF3-4 (PAL-Seq) GSM1316823  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 3 (4-cell) to NF stage 4 (8-cell)  
WE - NF3-4 (Ribo-Seq) GSM1276564  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 3 (4-cell) to NF stage 4 (8-cell)  
WE - NF9 GSM1276565  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9  
WE - NF9 (PAL-Seq) GSM1316824  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9  
WE - NF9 (Ribo-Seq) GSM1276566  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9  
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Xtr   
Xla 

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