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Series GSE133585 Query DataSets for GSE133585
Status Public on Jan 17, 2020
Title The RNA N6-methyladenosine regulates chromatin remodeling and transcription [seq_nuclearRNA]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary The N6-methyladenosine (m6A) has been shown to regulate stability and translation of messenger RNA (mRNA) in various biological processes. Here, we show that the knockout of the m6A writer Mettl3 or a nuclear reader Ythdc1 in mouse embryonic stem cells (mESCs) induces chromatin openness and transcription activation in an m6A-dependent manner. We identified extensive m6A modifications on caRNAs (chromosome-associated RNAs, including promoter-associated RNAs, enhancer RNAs and repeats) that are installed by METTL3. YTHDC1 can bind to a portion of these m6A-modified RNAs and facilitate their decay through the NEXT-mediated nuclear degradation. Therefore, the m6A methylation of these caRNAs reduces their abundances. The knockout of Mettl3 elevates levels of caRNAs and promote open chromatin state and downstream transcription. Collectively, our results reveal that m6A on caRNAs can globally tune chromatin state and transcription.
Overall design Examine nuclear non-ribosome RNA decay in ckoYTHDC1 and control mESCs, and gene expression in control and two knockout METTL3 mESCs
Contributor(s) Liu J, Dou X, He C
Citation(s) 31949099
Submission date Jul 01, 2019
Last update date Feb 10, 2020
Contact name Chuan He
Phone 773-702-5061
Organization name University of Chicago
Department Department of Chemistry
Street address 929 E 57th St., GCIS E319
City Chicago
State/province ILLINOIS
ZIP/Postal code 60637
Country USA
Platforms (2)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (18)
GSM3912543 Ythdc1_Control_0h_r1
GSM3912544 Ythdc1_Control_0h_r2
GSM3912545 Ythdc1_Control_3h_r1
This SubSeries is part of SuperSeries:
GSE133600 The RNA N6-methyladenosine regulates chromatin remodeling and transcription
BioProject PRJNA551966
SRA SRP212677

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

Supplementary file Size Download File type/resource
GSE133585_RAW.tar 3.9 Mb (http)(custom) TAR (of TXT)
GSE133585_htseq.gene.count.txt.gz 928.6 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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