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Series GSE190945 Query DataSets for GSE190945
Status Public on Dec 15, 2023
Title 18S rRNA methyltransferase EMG1 non-enzymatically influence m6A in mRNA
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary Defects in ribosome biogenesis can trigger a battery of cellular events to alter gene expression and cell growth. 18S rRNA methyltransferase EMG1 is an important assembly factor in ribosome biogenesis. Here, we report that downregulation of EMG1 non-enzymatically leads to decreased N6-methyladensine (m6A) levels in polyadenylated RNA. We revealed the identities of the messenger RNAs with decreased m6A intensities upon EMG1 deficiency using m6A-IP-seq. This group of mRNAs significantly overlap with the CLIP targets of IGF2BP3, which is an m6A reader protein stabilizing m6A-containing transcripts. Furthermore, both RNA-seq and qRT-PCR results suggest that the expression level of this group of mRNAs significantly decreased upon EMG1 deficiency, possibly through the regulation of IGF2BP3. Gene ontology analysis suggests that this group of mRNAs function in a list of cell signaling pathways important for cell growth. These findings collectively suggest that decreased ribosome assembly may influence gene expression via decreasing m6A levels in mRNAs.
 
Overall design m6AIP-seq after knocking down Emg1 in N2a cells
 
Contributor(s) Liu KF, Elashal H, Shen H
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Submission date Dec 15, 2021
Last update date Dec 15, 2023
Contact name Kathy Liu
E-mail(s) liufg@pennmedicine.upenn.edu
Organization name University of Pennsylvania
Street address 415 curie blvd
City philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platforms (1)
GPL21626 NextSeq 550 (Mus musculus)
Samples (8)
GSM5736057 siEmg1_m6AIP-seq_rep1
GSM5736058 siEmg1_m6AIP-seq_rep2
GSM5736059 siCtrl_m6AIP-seq_rep1
Relations
BioProject PRJNA789157
SRA SRP351315

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
GSE190945_DEseq2.txt.gz 882.0 Kb (ftp)(http) TXT
GSE190945_diff_m6A_peaks.xls.gz 87.2 Kb (ftp)(http) XLS
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Raw data are available in SRA
Processed data are available on Series record

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