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Series GSE139812 Query DataSets for GSE139812
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
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.
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.
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
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
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
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)
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
BioProject PRJNA587069
SRA SRP227923

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE139812_RNA-seq_normalized_counts.txt.gz 1.2 Mb (ftp)(http) TXT
GSE139812_RNA-seq_raw_counts.txt.gz 847.8 Kb (ftp)(http) TXT
GSE139812_snoRNAs.fa.gz 20.1 Kb (ftp)(http) FA
GSE139812_snoRNAs_normalized_counts.txt.gz 4.0 Kb (ftp)(http) TXT
GSE139812_snoRNAs_raw_counts.txt.gz 1.4 Kb (ftp)(http) TXT
GSE139812_snoRNAs_tx2gene.txt.gz 1.5 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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