Eisen et al. 2020 (PRJNA556006)
General Details
Title | The Dynamics of Cytoplasmic mRNA Metabolism |
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Organism | |
Number of Samples | 52 |
Release Date | 2019/07/22 00:00 |
Sequencing Types | |
Protocol Details |
Study Links
GWIPS-viz | Trips-Viz |
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Repository Details
SRA | SRP215938 |
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ENA | SRP215938 |
GEO | GSE134660 |
BioProject | PRJNA556006 |
Publication
Title | |
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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) | ||
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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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