|
| Status |
Public on Feb 10, 2020 |
| Title |
The RNA N6-methyladenosine regulates chromatin remodeling and transcription [HEC-1-A_seq_RNA_MeRIP] |
| Organism |
Homo sapiens |
| Experiment type |
Methylation 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.
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| |
|
| Overall design |
chromatin-associated RNA m6A profiles of METTL3 knockdown HEC-1-A and its control were generated by deep sequencing, in diplicate, using Illumina NovaSeq.
|
| |
|
| 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 |
| E-mail(s) |
chuanhe@uchicago.edu
|
| 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 (8)
|
| GSM4174095 |
METTL3_Control_Input_r1 [HEC-1-A: MeRIP] |
| GSM4174096 |
METTL3_Control_Input_r2 [HEC-1-A: MeRIP] |
| GSM4174097 |
METTL3_KD_Input_r1 [HEC-1-A: MeRIP] |
|
| This SubSeries is part of SuperSeries: |
| GSE140561 |
The RNA N6-methyladenosine regulates chromatin remodeling and transcription [HEC-1-A_seq] |
|
| Relations |
| BioProject |
PRJNA590170 |
| SRA |
SRP230409 |
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