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| Status |
Public on Aug 04, 2023 |
| Title |
Post-transcriptional regulation of Ribosome Biogenesis during differentiation [SLAM-seq] |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The regulation of ribosome biogenesis is a critical component of cell differentiation. Although ribosome biogenesis is well known to be regulated at the transcriptional level, its post-transcriptional regulation is less well understood. A key component of RNA post-transcriptional regulation is transcript decay rate which, together with the rate of synthesis, defines the abundance of the transcripts. Here we measured the stability of the whole transcriptome of P19 cells before differentiation (D0) and six days after the onset of differentiation (D6). We found that while global decay rates dropped during differentiation, the stability of transcripts encoding for ribosomal proteins remains significantly high throughout the differentiation process. These results indicate a strong and specific post-transcriptional regulation of ribosome biogenesis transcripts that is sustained during cell differentiation.
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| Overall design |
We prepared SLAM-seq catabolic and anabolic libraries for P19 undifferentiated and differentiated cells (4 experiments total). For each experiment, we collected biological duplicates or triplicates at time points 0, 3, 6, and 9 hrs after the removal of 4sU (catabolic experiment) or addition of the 4sU (anabolic experiment), and for each sample, we prepared an RNA seq library. Reads were mapped to the transcriptome, and uracil to cytosine conversions were quantified using the SLAMdunk software. The change in the U to C conversion from 0 to 9 hrs was used to calculate the decay or synthesis half-life of each transcript.
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| Contributor(s) |
Baptissart M, Papas BN, Morgan M |
| Citation(s) |
37636056 |
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| Submission date |
Oct 05, 2022 |
| Last update date |
Sep 14, 2023 |
| Contact name |
Marcos Morgan |
| Organization name |
NIEHS
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| Street address |
111 TW Alexander Dr
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| City |
Durham |
| ZIP/Postal code |
27709 |
| Country |
USA |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (47)
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| This SubSeries is part of SuperSeries: |
| GSE214875 |
Post-transcriptional regulation of Ribosome Biogenesis during differentiation |
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| Relations |
| BioProject |
PRJNA887409 |
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