Subtelny et al. 2015 (PRJNA230112)

General Details

Title Poly(A)-tail profiling reveals an embryonic switch in translational control
Organism
Number of Samples 24
Release Date 2013/11/27 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP033369
ENA SRP033369
GEO
BioProject PRJNA230112

Publication

Title
Authors Subtelny AO,Eichhorn SW,Chen GR,Sive H,Bartel DP
Journal Nature
Publication Date 2014 Apr 3
Abstract 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.
PMC PMC4086860
PMID 24476825
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR1146552 PRJNA230112 Mus musculus 3T3 Ribo-Seq
SRR1146553 PRJNA230112 Mus musculus 3T3 Ribo-Seq
SRR1146554 PRJNA230112 Mus musculus 3T3 Ribo-Seq
SRR1146555 PRJNA230112 Mus musculus 3T3 Ribo-Seq
SRR1146556 PRJNA230112 Mus musculus 3T3 Ribo-Seq
SRR1146557 PRJNA230112 Mus musculus 3T3 Ribo-Seq
SRR1146558 PRJNA230112 Mus musculus 3T3 Ribo-Seq
SRR1146559 PRJNA230112 Mus musculus 3T3 Ribo-Seq
SRR1039857 PRJNA230112 Schizosaccharomyces pombe Ribo-Seq
SRR1039859 PRJNA230112 Mus musculus Ribo-Seq
SRR1039861 PRJNA230112 Homo sapiens HEK293 Ribo-Seq Cycloheximide
SRR1039863 PRJNA230112 Mus musculus 3T3 Ribo-Seq
SRR1039873 PRJNA230112 Danio rerio Ribo-Seq
SRR1039874 PRJNA230112 Danio rerio Ribo-Seq
SRR1039875 PRJNA230112 Danio rerio Ribo-Seq
SRR1039876 PRJNA230112 Danio rerio Ribo-Seq
SRR1039877 PRJNA230112 Danio rerio Ribo-Seq
SRR1039878 PRJNA230112 Danio rerio Ribo-Seq
SRR1039879 PRJNA230112 Danio rerio Ribo-Seq
SRR1039880 PRJNA230112 Danio rerio Ribo-Seq
SRR1039881 PRJNA230112 Danio rerio Ribo-Seq
SRR1146618 PRJNA230112 Xenopus laevis Ribo-Seq
SRR1146615 PRJNA230112 Xenopus laevis Ribo-Seq
SRR1146574 PRJNA230112 Xenopus laevis Ribo-Seq
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)

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