Eisen et al. 2020 (PRJNA556006)

General Details

Title The Dynamics of Cytoplasmic mRNA Metabolism
Organism
Number of Samples 52
Release Date 2019/07/22 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP215938
ENA SRP215938
GEO GSE134660
BioProject PRJNA556006

Publication

Title
Authors Eisen TJ,Eichhorn SW,Subtelny AO,Lin KS,McGeary SE,Gupta S,Bartel DP
Journal Molecular cell
Publication Date 2020 Feb 20
Abstract For all but a few mRNAs, the dynamics of metabolism are unknown. Here, we developed an experimental and analytical framework for examining these dynamics for mRNAs from thousands of genes. mRNAs of mouse fibroblasts exit the nucleus with diverse intragenic and intergenic poly(A)-tail lengths. Once in the cytoplasm, they have a broad (1000-fold) range of deadenylation rate constants, which correspond to cytoplasmic lifetimes. Indeed, with few exceptions, degradation appears to occur primarily through deadenylation-linked mechanisms, with little contribution from either endonucleolytic cleavage or deadenylation-independent decapping. Most mRNA molecules degrade only after their tail lengths fall below 25 nt. Decay rate constants of short-tailed mRNAs vary broadly (1000-fold) and are larger for short-tailed mRNAs that have previously undergone more rapid deadenylation. This coupling helps clear rapidly deadenylated mRNAs, enabling the large range in deadenylation rate constants to impart a similarly large range in stabilities. Copyright © 2019 Elsevier Inc. All rights reserved.
PMC PMC7265681
PMID 31902669
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR9730186 PRJNA556006 Mus musculus 3T3 RNA-Seq
SRR9730187 PRJNA556006 Mus musculus 3T3 Ribo-Seq
SRR9730189 PRJNA556006 Mus musculus 3T3 RNA-Seq
SRR9730190 PRJNA556006 Mus musculus 3T3 Ribo-Seq
SRR9730192 PRJNA556006 Mus musculus 3T3 RNA-Seq
SRR9730193 PRJNA556006 Mus musculus 3T3 Ribo-Seq
SRR9730195 PRJNA556006 Mus musculus 3T3 RNA-Seq
SRR9730196 PRJNA556006 Mus musculus 3T3 Ribo-Seq
SRR9730198 PRJNA556006 Mus musculus 3T3 RNA-Seq
SRR9730199 PRJNA556006 Mus musculus 3T3 Ribo-Seq
SRR9730200 PRJNA556006 Mus musculus 3T3 Ribo-Seq
SRR9730202 PRJNA556006 Mus musculus 3T3 RNA-Seq
SRR9730203 PRJNA556006 Mus musculus 3T3 Ribo-Seq
SRR9730204 PRJNA556006 Mus musculus 3T3 RNA-Seq
SRR9730205 PRJNA556006 Mus musculus 3T3 Ribo-Seq
SRR9730206 PRJNA556006 Mus musculus 3T3 RNA-Seq
SRR9730207 PRJNA556006 Mus musculus 3T3 Ribo-Seq
SRR9730209 PRJNA556006 Mus musculus 3T3 RNA-Seq
SRR9730210 PRJNA556006 Mus musculus 3T3 Ribo-Seq
SRR9730212 PRJNA556006 Mus musculus 3T3 RNA-Seq
SRR9730213 PRJNA556006 Mus musculus 3T3 RNA-Seq
SRR9730214 PRJNA556006 Mus musculus 3T3 Ribo-Seq
SRR9730215 PRJNA556006 Mus musculus 3T3 RNA-Seq
SRR9730216 PRJNA556006 Mus musculus 3T3 Ribo-Seq
SRR9730150 PRJNA556006 Mus musculus 3T3 RNA-Seq
SRR9730151 PRJNA556006 Mus musculus 3T3 Ribo-Seq
SRR9730153 PRJNA556006 Mus musculus 3T3 RNA-Seq
SRR9730218 PRJNA556006 Mus musculus 3T3 RNA-Seq
SRR9730219 PRJNA556006 Mus musculus 3T3 Ribo-Seq
SRR9730221 PRJNA556006 Mus musculus 3T3 RNA-Seq
SRR9730222 PRJNA556006 Mus musculus 3T3 Ribo-Seq
SRR9730154 PRJNA556006 Mus musculus 3T3 Ribo-Seq
SRR9730156 PRJNA556006 Mus musculus 3T3 RNA-Seq
SRR9730157 PRJNA556006 Mus musculus 3T3 Ribo-Seq
SRR9730159 PRJNA556006 Mus musculus 3T3 RNA-Seq
SRR9730160 PRJNA556006 Mus musculus 3T3 Ribo-Seq
SRR9730162 PRJNA556006 Mus musculus 3T3 RNA-Seq
SRR9730163 PRJNA556006 Mus musculus 3T3 Ribo-Seq
SRR9730165 PRJNA556006 Mus musculus 3T3 RNA-Seq
SRR9730166 PRJNA556006 Mus musculus 3T3 Ribo-Seq
SRR9730168 PRJNA556006 Mus musculus 3T3 RNA-Seq
SRR9730169 PRJNA556006 Mus musculus 3T3 Ribo-Seq
SRR9730171 PRJNA556006 Mus musculus 3T3 RNA-Seq
SRR9730172 PRJNA556006 Mus musculus 3T3 Ribo-Seq
SRR9730174 PRJNA556006 Mus musculus 3T3 RNA-Seq
SRR9730175 PRJNA556006 Mus musculus 3T3 Ribo-Seq
SRR9730177 PRJNA556006 Mus musculus 3T3 RNA-Seq
SRR9730178 PRJNA556006 Mus musculus 3T3 Ribo-Seq
SRR9730180 PRJNA556006 Mus musculus 3T3 RNA-Seq
SRR9730181 PRJNA556006 Mus musculus 3T3 Ribo-Seq
SRR9730183 PRJNA556006 Mus musculus 3T3 RNA-Seq
SRR9730184 PRJNA556006 Mus musculus 3T3 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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