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Series GSE140560 Query DataSets for GSE140560
Status Public on Feb 10, 2020
Title The RNA N6-methyladenosine regulates chromatin remodeling and transcription [HEC-1-A_seq_RNA_nuclear]
Organism Homo sapiens
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 gene expression in control and METTL3 knockdown HEC-1-A cells
Contributor(s) Liu J, Dou X, He C
Citation(s) 31949099
Submission date Nov 18, 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 (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (4)
GSM4174167 METTL3_Control_nuclearRNA_r1 [HEC-1-A]
GSM4174168 METTL3_Control_nuclearRNA_r2 [HEC-1-A]
GSM4174169 METTL3_KD_nuclearRNA_r1 [HEC-1-A]
This SubSeries is part of SuperSeries:
GSE140561 The RNA N6-methyladenosine regulates chromatin remodeling and transcription [HEC-1-A_seq]
BioProject PRJNA590182
SRA SRP230413

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

Supplementary file Size Download File type/resource
GSE140560_RAW.tar 990.0 Kb (http)(custom) TAR (of TXT)
GSE140560_htseq.gene.count.txt.gz 430.1 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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