Ries et al. 2019 (PRJNA517401)
General Details
| Title | RNA-seq and ribosome profiling of heat shocked wild type and Mettl14 -/- mouse embryonic stem cells |
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| Organism | |
| Number of Samples | 24 |
| Release Date | 2019/01/28 00:00 |
| Sequencing Types | |
| Protocol Details |
Study Links
| GWIPS-viz | Trips-Viz |
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Repository Details
| SRA | SRP182641 |
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| ENA | SRP182641 |
| GEO | |
| BioProject | PRJNA517401 |
Publication
| Title | |
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| Authors | Ries RJ,Zaccara S,Klein P,Olarerin-George A,Namkoong S,Pickering BF,Patil DP,Kwak H,Lee JH,Jaffrey SR |
| Journal | Nature |
| Publication Date | 2019 Jul |
| Abstract | N 6 -methyladenosine (m 6 A) is the most prevalent modified nucleotide in mRNA 1,2 , with around 25% of mRNAs containing at least one m 6 A. Methylation of mRNA to form m 6 A is required for diverse cellular and physiological processes 3 . Although the presence of m 6 A in an mRNA can affect its fate in different ways, it is unclear how m 6 A directs this process and why the effects of m 6 A can vary in different cellular contexts. Here we show that the cytosolic m 6 A-binding proteins-YTHDF1, YTHDF2 and YTHDF3-undergo liquid-liquid phase separation in vitro and in cells. This phase separation is markedly enhanced by mRNAs that contain multiple, but not single, m 6 A residues. Polymethylated mRNAs act as a multivalent scaffold for the binding of YTHDF proteins, juxtaposing their low-complexity domains and thereby leading to phase separation. The resulting mRNA-YTHDF complexes then partition into different endogenous phase-separated compartments, such as P-bodies, stress granules or neuronal RNA granules. m 6 A-mRNA is subject to compartment-specific regulation, including a reduction in the stability and translation of mRNA. These studies reveal that the number and distribution of m 6 A sites in cellular mRNAs can regulate and influence the composition of the phase-separated transcriptome, and suggest that the cellular properties of m 6 A-modified mRNAs are governed by liquid-liquid phase separation principles. |
| PMC | PMC6662915 |
| PMID | 31292544 |
| 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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| SRR8494660 | PRJNA517401 | Mus musculus | mouse embryonic stem cells | Ribo-Seq | Cycloheximide |  |
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| SRR8494662 | PRJNA517401 | Mus musculus | mouse embryonic stem cells | Ribo-Seq | Cycloheximide | |
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| SRR8494664 | PRJNA517401 | Mus musculus | mouse embryonic stem cells | Ribo-Seq | Cycloheximide | |
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| SRR8494666 | PRJNA517401 | Mus musculus | mouse embryonic stem cells | Ribo-Seq | Cycloheximide | |
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| SRR8494668 | PRJNA517401 | Mus musculus | mouse embryonic stem cells | Ribo-Seq | Cycloheximide | |
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| SRR8494670 | PRJNA517401 | Mus musculus | mouse embryonic stem cells | Ribo-Seq | Cycloheximide | |
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| SRR8494672 | PRJNA517401 | Mus musculus | mouse embryonic stem cells | Ribo-Seq | Cycloheximide | |
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| SRR8494674 | PRJNA517401 | Mus musculus | mouse embryonic stem cells | Ribo-Seq | Cycloheximide | |
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| SRR8494676 | PRJNA517401 | Mus musculus | mouse embryonic stem cells | Ribo-Seq | Cycloheximide | |
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| SRR8494678 | PRJNA517401 | Mus musculus | mouse embryonic stem cells | Ribo-Seq | Cycloheximide | |
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| SRR8494680 | PRJNA517401 | Mus musculus | mouse embryonic stem cells | Ribo-Seq | Cycloheximide | |
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| SRR8494682 | PRJNA517401 | Mus musculus | mouse embryonic stem cells | Ribo-Seq | Cycloheximide | |
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| SRR8494684 | PRJNA517401 | Mus musculus | mouse embryonic stem cells | Ribo-Seq | Cycloheximide | |
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| SRR8494686 | PRJNA517401 | Mus musculus | mouse embryonic stem cells | Ribo-Seq | Cycloheximide | |
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| SRR8494688 | PRJNA517401 | Mus musculus | mouse embryonic stem cells | Ribo-Seq | Cycloheximide | |
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| SRR8494690 | PRJNA517401 | Mus musculus | mouse embryonic stem cells | Ribo-Seq | Cycloheximide | |
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| SRR8494692 | PRJNA517401 | Mus musculus | mouse embryonic stem cells | Ribo-Seq | Cycloheximide | |
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| SRR8494694 | PRJNA517401 | Mus musculus | mouse embryonic stem cells | Ribo-Seq | Cycloheximide | |
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| SRR8494696 | PRJNA517401 | Mus musculus | mouse embryonic stem cells | Ribo-Seq | Cycloheximide | |
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| SRR8494698 | PRJNA517401 | Mus musculus | mouse embryonic stem cells | Ribo-Seq | Cycloheximide | |
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| SRR8494700 | PRJNA517401 | Mus musculus | mouse embryonic stem cells | Ribo-Seq | Cycloheximide | |
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| SRR8494702 | PRJNA517401 | Mus musculus | mouse embryonic stem cells | Ribo-Seq | Cycloheximide | |
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| SRR8494704 | PRJNA517401 | Mus musculus | mouse embryonic stem cells | Ribo-Seq | Cycloheximide | |
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| SRR8494706 | PRJNA517401 | Mus musculus | mouse embryonic stem cells | Ribo-Seq | Cycloheximide | |
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| 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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