|
| Status |
Public on Apr 02, 2018 |
| Title |
A somatic role for the histone methyltransferase Setdb1 in endogenous retrovirus silencing [ChIP-Seq] |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Subsets of endogenous retroviruses (ERVs) are derepressed in mouse embryonic stem cells (mESCs) deficient for Setdb1, which catalyzes histone H3 lysine 9 trimethylation (H3K9me3). Most of those ERVs, including IAPs, remain silent if Setdb1 is deleted in differentiated embryonic cells; however they are derepressed when deficient for Dnmt1, suggesting that Setdb1 is dispensable for ERV silencing in somatic cells. However, H3K9me3 enrichment on ERVs is maintained in differentiated cells and is mostly diminished in mouse embryonic fibroblasts (MEFs) lacking Setdb1. We find that distinctive sets of ERVs are reactivated in different types of Setdb1-deficient somatic cells, including the VL30-class of ERVs in MEFs, whose derepression is dependent on cell type-specific transcription factors (TFs). These data suggest a more general role for Setdb1 in ERV silencing, which provides an additional layer of epigenetic silencing through the H3K9me3 modification.
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| |
|
| Overall design |
Analyses of transcriptional profiles and chromatin state in Setdb1 WT and KO cells
|
| |
|
| Contributor(s) |
Kato M, Takemoto K, Shinkai Y |
| Citation(s) |
29703894 |
| |
| Submission date |
Aug 10, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Masaki Kato |
| E-mail(s) |
mkato@riken.jp
|
| Organization name |
RIKEN
|
| Lab |
Cellular Memory Laboratory
|
| Street address |
2-1 Hirosawa
|
| City |
Wako |
| State/province |
Saitama |
| ZIP/Postal code |
3510198 |
| Country |
Japan |
| |
|
| Platforms (1) |
| GPL18480 |
Illumina HiSeq 1500 (Mus musculus) |
|
| Samples (7)
|
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| This SubSeries is part of SuperSeries: |
| GSE102490 |
A somatic role for the histone methyltransferase Setdb1 in endogenous retrovirus silencing |
|
| Relations |
| BioProject |
PRJNA398189 |
| SRA |
SRP115381 |
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