Popa et al. 2016 (PRJNA280809)

General Details

Title Ribosome profiling with translation inhibitors reveals pervasive translation in murine ES cells
Organism
Number of Samples 24
Release Date 2015/04/10 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP057051
ENA SRP057051
GEO
BioProject PRJNA280809

Publication

Title
Authors Popa A,Lebrigand K,Barbry P,Waldmann R
Journal BMC genomics
Publication Date 2016 Jan 14
Abstract Open reading frames are common in long noncoding RNAs (lncRNAs) and 5'UTRs of protein coding transcripts (uORFs). The question of whether those ORFs are translated was recently addressed by several groups using ribosome profiling. Most of those studies concluded that certain lncRNAs and uORFs are translated, essentially based on computational analysis of ribosome footprints. However, major discrepancies remain on the scope of translation and the translational status of individual ORFs. In consequence, further criteria are required to reliably identify translated ORFs from ribosome profiling data. We examined the effect of the translation inhibitors pateamine A, harringtonine and puromycin on murine ES cell ribosome footprints. We found that pateamine A, a drug that targets eIF4A, allows a far more accurate identification of translated sequences than previously used drugs and computational scoring schemes. Our data show that at least one third but less than two thirds of ES cell lncRNAs are translated. We also identified translated uORFs in hundreds of annotated coding transcripts including key pluripotency transcripts, such as dicer, lin28, trim71, and ctcf. Pateamine A inhibition data clearly increase the precision of the detection of translated ORFs in ribosome profiling experiments. Our data show that translation of lncRNAs and uORFs in murine ES cells is rather common although less pervasive than previously suggested. The observation of translated uORFs in several key pluripotency transcripts suggests that translational regulation by uORFs might be part of the network that defines mammalian stem cell identity.
PMC PMC4712605
PMID 26764022
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR1964306 PRJNA280809 Mus musculus CGR8 Ribo-Seq
SRR1964307 PRJNA280809 Mus musculus CGR8 Ribo-Seq
SRR1964308 PRJNA280809 Mus musculus CGR8 Ribo-Seq Harringtonine
SRR1964309 PRJNA280809 Mus musculus CGR8 Ribo-Seq Harringtonine
SRR1964310 PRJNA280809 Mus musculus CGR8 Ribo-Seq
SRR1964311 PRJNA280809 Mus musculus CGR8 Ribo-Seq
SRR1964312 PRJNA280809 Mus musculus CGR8 Ribo-Seq
SRR1964313 PRJNA280809 Mus musculus CGR8 Ribo-Seq
SRR1964314 PRJNA280809 Mus musculus CGR8 Ribo-Seq Harringtonine
SRR1964315 PRJNA280809 Mus musculus CGR8 Ribo-Seq Harringtonine
SRR1964316 PRJNA280809 Mus musculus CGR8 Ribo-Seq Harringtonine
SRR1964317 PRJNA280809 Mus musculus CGR8 Ribo-Seq Harringtonine
SRR1964318 PRJNA280809 Mus musculus CGR8 Ribo-Seq Harringtonine
SRR1964319 PRJNA280809 Mus musculus CGR8 Ribo-Seq Harringtonine
SRR1964320 PRJNA280809 Mus musculus CGR8 Ribo-Seq
SRR1964321 PRJNA280809 Mus musculus CGR8 Ribo-Seq
SRR1964322 PRJNA280809 Mus musculus CGR8 Ribo-Seq
SRR1964323 PRJNA280809 Mus musculus CGR8 Ribo-Seq
SRR1964324 PRJNA280809 Mus musculus CGR8 Ribo-Seq
SRR1964325 PRJNA280809 Mus musculus CGR8 Ribo-Seq
SRR1964326 PRJNA280809 Mus musculus CGR8 Ribo-Seq
SRR1964327 PRJNA280809 Mus musculus CGR8 Ribo-Seq
SRR1964328 PRJNA280809 Mus musculus CGR8 Ribo-Seq Harringtonine
SRR1964329 PRJNA280809 Mus musculus CGR8 Ribo-Seq Harringtonine
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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