Tuck et al. 2020 (PRJNA553494)

General Details

Title Mammalian RNA decay pathways are highly specialized and widely linked to translation
Organism
Number of Samples 24
Release Date 2019/07/09 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP213860
ENA SRP213860
GEO GSE134020
BioProject PRJNA553494

Publication

Title
Authors Tuck AC,Rankova A,Arpat AB,Liechti LA,Hess D,Iesmantavicius V,Castelo-Szekely V,Gatfield D,Bühler M
Journal Molecular cell
Publication Date 2020 Mar 19
Abstract RNA decay is crucial for mRNA turnover and surveillance and misregulated in many diseases. This complex system is challenging to study, particularly in mammals, where it remains unclear whether decay pathways perform specialized versus redundant roles. Cytoplasmic pathways and links to translation are particularly enigmatic. By directly profiling decay factor targets and normal versus aberrant translation in mouse embryonic stem cells (mESCs), we uncovered extensive decay pathway specialization and crosstalk with translation. XRN1 (5'-3') mediates cytoplasmic bulk mRNA turnover whereas SKIV2L (3'-5') is universally recruited by ribosomes, tackling aberrant translation and sometimes modulating mRNA abundance. Further exploring translation surveillance revealed AVEN and FOCAD as SKIV2L interactors. AVEN prevents ribosome stalls at structured regions, which otherwise require SKIV2L for clearance. This pathway is crucial for histone translation, upstream open reading frame (uORF) regulation, and counteracting ribosome arrest on small ORFs. In summary, we uncovered key targets, components, and functions of mammalian RNA decay pathways and extensive coupling to translation. Copyright © 2020 The Author(s). Published by Elsevier Inc. All rights reserved.
PMC PMC7083229
PMID 32048998
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR9693934 PRJNA553494 Mus musculus Ribo-Seq
SRR9693935 PRJNA553494 Mus musculus Ribo-Seq
SRR9693936 PRJNA553494 Mus musculus Ribo-Seq
SRR9693937 PRJNA553494 Mus musculus Ribo-Seq
SRR9693938 PRJNA553494 Mus musculus Ribo-Seq
SRR9693939 PRJNA553494 Mus musculus Ribo-Seq
SRR9693940 PRJNA553494 Mus musculus Ribo-Seq
SRR9693941 PRJNA553494 Mus musculus Ribo-Seq
SRR9693966 PRJNA553494 Mus musculus RNA-Seq
SRR9693967 PRJNA553494 Mus musculus RNA-Seq
SRR9693968 PRJNA553494 Mus musculus RNA-Seq
SRR9693969 PRJNA553494 Mus musculus RNA-Seq
SRR9693970 PRJNA553494 Mus musculus RNA-Seq
SRR9693971 PRJNA553494 Mus musculus RNA-Seq
SRR9693972 PRJNA553494 Mus musculus RNA-Seq
SRR9693973 PRJNA553494 Mus musculus RNA-Seq
SRR9693974 PRJNA553494 Mus musculus RNA-Seq
SRR9693975 PRJNA553494 Mus musculus RNA-Seq
SRR9693976 PRJNA553494 Mus musculus RNA-Seq
SRR9693977 PRJNA553494 Mus musculus RNA-Seq
SRR9693978 PRJNA553494 Mus musculus RNA-Seq
SRR9693979 PRJNA553494 Mus musculus RNA-Seq
SRR9693980 PRJNA553494 Mus musculus RNA-Seq
SRR9693981 PRJNA553494 Mus musculus RNA-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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