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| Status |
Public on Mar 18, 2021 |
| Title |
Regulation of 3D genome organization, transcription and histone H3K9me2 by histone H3K9 methyltransferases [RNA-Seq] |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Histone H3 lysine 9 dimethylation (H3K9me2) is a highly conserved silencing epigenetic mark. Chromatin marked with H3K9me2 forms large domains in mammalian cells and overlaps well with lamina-associated domains and the B compartment defined by Hi-C. However, the role of H3K9me2 in 3-dimensional (3D) genome organization remains unclear. We investigated genome-wide H3K9me2 distribution, transcriptome, and 3D genome organization in mouse embryonic stem cells following the inhibition or depletion of five H3K9 methyltransferases (MTases): G9a, GLP, SETDB1, SUV39H1, and SUV39H2. H3K9me2 was regulated by all five MTases; however, H3K9me2 and transcription in the A and B compartments were regulated by different MTases. H3K9me2 in A compartments was primarily regulated by G9a/GLP and SETDB1, while H3K9me2 in the B compartments was regulated by all five MTases. Furthermore, decreased H3K9me2 correlated with changes to the more active compartmental state that accompanied transcriptional activation.
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| Overall design |
Examination of H3K9me2, H3K9me3, transcriptome and 3D genome organization in H3K9 methyltransferase deficient mESCs and iMEFs
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| Contributor(s) |
Fukuda K, Shinkai Y |
| Citation(s) |
33986449 |
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| Submission date |
Mar 17, 2021 |
| Last update date |
May 25, 2021 |
| Contact name |
Kei Fukuda |
| E-mail(s) |
kefukuda8@gmail.com
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| Organization name |
RIKEN
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| Lab |
Cellular memory
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| Street address |
2-1 Hrosawa, Wakoshi
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| City |
Saitama |
| State/province |
Japan |
| ZIP/Postal code |
351-0198 |
| Country |
Japan |
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| Platforms (1) |
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| Samples (8)
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| This SubSeries is part of SuperSeries: |
| GSE169106 |
Regulation of 3D genome organization, transcription and histone H3K9me2 by histone H3K9 methyltransferases |
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| Relations |
| BioProject |
PRJNA715207 |
| SRA |
SRP311083 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE169098_RAW.tar |
890.0 Kb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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