Stadler et al. 2013 (PRJNA208993)

General Details

Title mRNA and Ribosome Profiling in Four Nematode Species Traversing a Shared Developmental Transition
Organism
Number of Samples 24
Release Date 2013/06/20 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP026198
ENA SRP026198
GEO 0.0
BioProject PRJNA208993

Publication

Title
Authors Stadler M, Fire A
Journal PLoS genetics
Publication Date 2013
Abstract Nematodes of the genus Caenorhabditis enter a developmental diapause state after hatching in the absence of food. To better understand the relative contributions of distinct regulatory modalities to gene expression changes associated with this developmental transition, we characterized genome-wide changes in mRNA abundance and translational efficiency associated with L1 diapause exit in four species using ribosome profiling and mRNA-seq. We found a strong tendency for translational regulation and mRNA abundance processes to act synergistically, together effecting a dramatic remodeling of the gene expression program. While gene-specific differences were observed between species, overall translational dynamics were broadly and functionally conserved. A striking, conserved feature of the response was strong translational suppression of ribosomal protein production during L1 diapause, followed by activation upon resumed development. On a global scale, ribosome footprint abundance changes showed greater similarity between species than changes in mRNA abundance, illustrating a substantial and genome-wide contribution of translational regulation to evolutionary maintenance of stable gene expression.
PMC PMC3789828
PMID 24098135
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR914334 PRJNA208993 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR914335 PRJNA208993 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR914336 PRJNA208993 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR914337 PRJNA208993 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR914338 PRJNA208993 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR914339 PRJNA208993 Caenorhabditis elegans 0.0 Ribo-Seq 0.0
SRR914346 PRJNA208993 Caenorhabditis briggsae 0.0 Ribo-Seq 0.0
SRR914347 PRJNA208993 Caenorhabditis briggsae 0.0 Ribo-Seq 0.0
SRR914348 PRJNA208993 Caenorhabditis briggsae 0.0 Ribo-Seq 0.0
SRR914349 PRJNA208993 Caenorhabditis briggsae 0.0 Ribo-Seq 0.0
SRR914350 PRJNA208993 Caenorhabditis briggsae 0.0 Ribo-Seq 0.0
SRR914351 PRJNA208993 Caenorhabditis briggsae 0.0 Ribo-Seq 0.0
SRR914358 PRJNA208993 Caenorhabditis remanei 0.0 Ribo-Seq 0.0
SRR914359 PRJNA208993 Caenorhabditis remanei 0.0 Ribo-Seq 0.0
SRR914360 PRJNA208993 Caenorhabditis remanei 0.0 Ribo-Seq 0.0
SRR914361 PRJNA208993 Caenorhabditis remanei 0.0 Ribo-Seq 0.0
SRR914362 PRJNA208993 Caenorhabditis remanei 0.0 Ribo-Seq 0.0
SRR914363 PRJNA208993 Caenorhabditis remanei 0.0 Ribo-Seq 0.0
SRR914370 PRJNA208993 Caenorhabditis brenneri 0.0 Ribo-Seq 0.0
SRR914371 PRJNA208993 Caenorhabditis brenneri 0.0 Ribo-Seq 0.0
SRR914372 PRJNA208993 Caenorhabditis brenneri 0.0 Ribo-Seq 0.0
SRR914373 PRJNA208993 Caenorhabditis brenneri 0.0 Ribo-Seq 0.0
SRR914374 PRJNA208993 Caenorhabditis brenneri 0.0 Ribo-Seq 0.0
SRR914375 PRJNA208993 Caenorhabditis brenneri 0.0 Ribo-Seq 0.0
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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