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| Status |
Public on Jul 09, 2020 |
| Title |
Regulated snoRNA expression during differentiation corresponds with a change in ribosomal RNA pseudouridylation and altered pre-ribosomal RNA processing [RNA-seq and ncRNA-seq] |
| Organism |
Mus musculus |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
Expression profiling by high throughput sequencing
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| Summary |
H/ACA small nucleolar RNAs (snoRNAs) guide pseudouridylation as part of a small nucleolar ribonucleoprotein complex (snoRNP). Disruption of H/ACA snoRNA expression in stem cells impairs pluripotency, yet it remains unclear how H/ACA snoRNAs contribute to differentiation. To determine if H/ACA snoRNA expression is dynamic during differentiation, we comprehensively profiled H/ACA snoRNA expression in multiple murine cell types and during differentiation in three cellular models, including mouse embryonic stem cells and mouse myoblasts. We determined that H/ACA snoRNA expression is cell-type specific, and we identified a subset of snoRNAs that are specifically regulated during differentiation. Additionally, we demonstrated that a decrease in Snora27 expression upon differentiation corresponds to a decrease in pseudouridylation of its target site within the E-site transfer RNA (tRNA) binding region of the 28S ribosomal RNA (rRNA) in the large ribosomal subunit. Many of the snoRNAs regulated during differentiation have target nucleotides in the 28S rRNA, and we found that pre-rRNA processing of large subunit precursors is altered during differentiation. Together, these data suggest a model in which H/ACA snoRNAs are specifically regulated during differentiation to potentially alter pseudouridylation and fine tune ribosome function.
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| Overall design |
In this study, we assessed expression of small RNAs in E14TG2a before and after differentiation with retinoic acid and we assessed gene expression in C2C12 cells before and after differentiation into myotubes.
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| Contributor(s) |
McCann KL, Kavari SL, Phillips BT, Burkholder AB, Hall TM |
| Citation(s) |
32710630 |
| |
| Submission date |
Nov 01, 2019 |
| Last update date |
Sep 15, 2020 |
| Contact name |
Kathleen McCann |
| E-mail(s) |
kathleen.mccann2@nih.gov
|
| Organization name |
National Institute of Environmental Health Sciences
|
| Street address |
111 TW Alexander Dr
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (12)
|
| GSM4146706 |
mESCs untreated T=0 rep1 (small RNA-seq) |
| GSM4146707 |
mESCs untreated T=0 rep2 (small RNA-seq) |
| GSM4146708 |
mESCs untreated T=0 rep3 (small RNA-seq) |
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| This SubSeries is part of SuperSeries: |
| GSE140623 |
Regulated snoRNA expression during differentiation corresponds with a change in ribosomal RNA pseudouridylation and altered pre-ribosomal RNA processing |
|
| Relations |
| BioProject |
PRJNA587069 |
| SRA |
SRP227923 |
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