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| Status |
Public on May 19, 2023 |
| Title |
m6A RNA methylation orchestrates transcriptional dormancy during paused pluripotency [RNA-seq] |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Development is often assumed to be a sequential unfolding of genetic programs towards increased complexity and occurring with a very stereotypical timing. However, embryos across all lineages of metazoans can enter reversible states of developmental pausing in response to adverse environmental conditions. In mammals, pausing manifests as a delayed implantation of the blastocyst, the source of embryonic stem cells (ESCs). Paused pluripotency can be induced in mouse blastocysts and ESCs by inhibition of mTOR, a conserved growth-promoting kinase, and is characterized by a drastic global decrease in biosynthetic activity, including gene transcription. The molecular mechanisms by which this remarkable dormant cellular state is achieved remain largely unknown. Here we show that m6A RNA methylation by Mettl3 is essential for transcriptional dormancy and maintenance of the paused pluripotent state in vitro and in vivo. Mass spectrometry and transcriptome-wide sequencing revealed an increase in m6A in paused ESCs. Knockout of the RNA methyltransferase Mettl3 suppresses transcriptional and proliferation dormancy of ESC specifically in the paused state, and leads to loss of paused blastocysts. Integration of several datasets in vitro and in vivo identified the transcriptional amplifier and oncogene Mycn as a key “anti-pausing factor” regulated by m6A mRNA methylation. Mett3-mediated methylation at a specific site of the Mycn mRNA is essential for its destabilization, which in turns mediates suppression of nascent transcription and proliferation in paused conditions. Our results highlight an intricate feedback between signaling, regulation of RNA stability and nascent transcription during pausing, with Mettl3 as an essential integrator and Mycn as a key downstream anti-pausing factor. These findings shed light on the mechanisms that underlie tuning of global transcriptional output during mammalian developmental pausing, and that may be redeployed in adult stem cells or during cancer dormancy.
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| Overall design |
Wildtype and Mettl3-KO mESCs were cultured under control (FBS/LIF) or paused (200nM INK128) conditions for 2 weeks and RNA-seq was performed.
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| Contributor(s) |
Ramalho-Santos M, Collignon E |
| Citation(s) |
37696947 |
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| Submission date |
May 12, 2022 |
| Last update date |
Sep 19, 2023 |
| Contact name |
Evelyne Anne Collignon |
| Organization name |
Lunenfeld-Tanenbaum Research Institute
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| Lab |
Ramalho-Santos lab
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| Street address |
60 Murray Street, Box42,
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| City |
Toronto |
| State/province |
ON |
| ZIP/Postal code |
M5T 3L9 |
| Country |
Canada |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (12)
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| GSM6134100 |
E14-Mettl3-KO, paused, rep1 |
| GSM6134101 |
E14-WT, FBS, rep2 |
| GSM6134102 |
E14-Mettl3-KO, FBS, rep2 |
| GSM6134103 |
E14-WT, paused, rep2 |
| GSM6134104 |
E14-Mettl3-KO, paused, rep2 |
| GSM6134105 |
E14-WT, FBS, rep3 |
| GSM6134106 |
E14-Mettl3-KO, FBS, rep3 |
| GSM6134107 |
E14-WT, paused, rep3 |
| GSM6134108 |
E14-Mettl3-KO, paused, rep3 |
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| This SubSeries is part of SuperSeries: |
| GSE202848 |
m6A RNA methylation orchestrates transcriptional dormancy during paused pluripotency |
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| Relations |
| BioProject |
PRJNA837543 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE202844_M3KO_RNAseq_logcounts_cell_number_normalized.txt.gz |
918.5 Kb |
(ftp)(http) |
TXT |
| GSE202844_M3KO_RNAseq_raw_counts_with_ERCCs.txt.gz |
436.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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