|
| Status |
Public on Jul 07, 2022 |
| Title |
Histone H3K36me2 and H3K36me3 form a chromatin platform essential for DNMT3A-dependent DNA methylation in mouse oocytes |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
|
| Summary |
Establishment of the DNA methylation landscape of mammalian oocytes, mediated by the DNMT3A-DNMT3L complex, is crucial for reproduction and development. In mouse oocytes, high levels of DNA methylation occur exclusively in the transcriptionally active regions, with moderate to low levels of methylation in other regions. Histone H3K36me3 mediates the high levels of methylation in the transcribed regions; however, it is unknown which histone mark guides the methylation in the other regions. Here, we show that, in mouse oocytes, H3K36me2 is highly enriched in the X chromosome and is broadly distributed across all autosomes. Upon H3K36me2 depletion, DNA methylation in moderately methylated regions is selectively affected, and a methylation pattern unique to the X chromosome is switched to an autosome-like pattern. Furthermore, we find that simultaneous depletion of H3K36me2 and H3K36me3 results in global hypomethylation, comparable to that of DNMT3A depletion. Therefore, the two histone marks jointly provide the chromatin platform essential for guiding DNMT3A-dependent DNA methylation in mouse oocytes.
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| Overall design |
ChIP-seq, CUT&RUN, WGBS were performed with mouse oocytes. RNA-seq was performed with oocytes or late 2-cell embryos.
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| Web link |
https://doi.org/10.1038/s41467-022-32141-2
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| Contributor(s) |
Yano S, Ishiuchi T, Abe S, Namekawa SH, Huang G, Ogawa Y, Sasaki H |
| Citation(s) |
35922445 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R35 GM141085 |
Epigenetic gene regulation in the germline |
UNIVERSITY OF CALIFORNIA DAVIS |
Satoshi Namekawa |
| R01 CA248019 |
The Role of HIF1A-DNMT3A axis in AML1/ETO-Driven Acute Myelogenous Leukemia |
UNIVERSITY OF MINNESOTA |
Gang Huang |
| R01 DK130478 |
Mechanism of the short- and long-term effects of COVID-19-induced Alarmins on hematopoietic stem and progenitor cells. |
UNIVERSITY OF KENTUCKY RESEARCH FOUNDATION |
Gang Huang |
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| |
| Submission date |
Sep 12, 2021 |
| Last update date |
Aug 04, 2022 |
| Contact name |
Hiroyuki Sasaki |
| E-mail(s) |
hsasaki@bioreg.kyushu-u.ac.jp
|
| Organization name |
Medical Institute of Bioregulation, Kyushu University
|
| Department |
Department of Molecular and Structural Biology
|
| Lab |
Division of Epigenomics and Development
|
| Street address |
3-1-1 Maidashi, Higashi-ku
|
| City |
Fukuoka |
| ZIP/Postal code |
812-8582 |
| Country |
Japan |
| |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (45)
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| Relations |
| BioProject |
PRJNA762552 |
| SRA |
SRP336725 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE183969_DNAme_DM_10kb.bw |
2.4 Mb |
(ftp)(http) |
BW |
| GSE183969_DNAme_K36M_10kb.bw |
2.4 Mb |
(ftp)(http) |
BW |
| GSE183969_DNAme_Setd2_KO_10kb.bw |
2.4 Mb |
(ftp)(http) |
BW |
| GSE183969_DNAme_ctrl_10kb.bw |
3.7 Mb |
(ftp)(http) |
BW |
| GSE183969_H3K27me3_K36M_rep1_10kb.bw |
2.2 Mb |
(ftp)(http) |
BW |
| GSE183969_H3K27me3_K36M_rep2_10kb.bw |
2.2 Mb |
(ftp)(http) |
BW |
| GSE183969_H3K27me3_ctrl_rep1_10kb.bw |
2.1 Mb |
(ftp)(http) |
BW |
| GSE183969_H3K27me3_ctrl_rep2_10kb.bw |
2.0 Mb |
(ftp)(http) |
BW |
| GSE183969_H3K36me2_K36M_rep1_scaled_10kb.bw |
2.4 Mb |
(ftp)(http) |
BW |
| GSE183969_H3K36me2_K36M_rep2_10kb.bw |
2.4 Mb |
(ftp)(http) |
BW |
| GSE183969_H3K36me2_ctrl_rep1_scaled_10kb.bw |
2.4 Mb |
(ftp)(http) |
BW |
| GSE183969_H3K36me2_ctrl_rep2_10kb.bw |
2.4 Mb |
(ftp)(http) |
BW |
| GSE183969_H3K36me3_K36M_scaled_10kb.bw |
3.6 Mb |
(ftp)(http) |
BW |
| GSE183969_H3K36me3_ctrl_scaled_10kb.bw |
2.4 Mb |
(ftp)(http) |
BW |
| GSE183969_TPM_FGO_2C.txt.gz |
2.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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