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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 19, 2017 |
| Title |
Rif1 Promotes a Repressive Chromatin State to Safeguard Against Endogenous Retrovirus Activation [MeDIP-seq] |
| Organism |
Mus musculus |
| Experiment type |
Methylation profiling by high throughput sequencing
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| Summary |
Transposable elements, including endogenous retroviruses (ERVs), constitute a large fraction of the mammalian genome. They are transcriptionally silenced during early development to protect genome integrity and aberrant transcription. However, the mechanisms that control their repression are not fully understood. To systematically study ERV repression, we carried out an RNAi screen in mouse embryonic stem cells (ESCs) and identified a list of novel regulators. Among them, Rif1 displays the strongest effect. Rif1 depletion by RNAi or gene deletion led to increased transcription and increased chromatin accessibility at ERV regions and their neighboring genes. This transcriptional de-repression becomes more severe when DNA methylation is lost. On the mechanistic level, Rif1 directly occupies ERVs and is required for repressive histone mark H3K9me3 and H3K27me3 assembly and DNA methylation. It interacts with histone methyltransferases and facilitates their recruitment to ERV regions. Importantly, Rif1 represses ERVs in human ESCs as well, and the evolutionally-conserved HEAT-like domain is essential for its function. Finally, Rif1 acts as a barrier during somatic cell reprogramming, and its depletion significantly enhances reprogramming efficiency. Together, our study uncovered many previously uncharacterized repressors of ERVs, and defined an essential role of Rif1 in the epigenetic defense against ERV activation.
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| Overall design |
ChIP-Seq profiling, RNA-Seq profiling, ATAC-seq profiling, MeDIP-seq profiling on mouse ES cells
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| Contributor(s) |
Li P, Bennett B, Hu G |
| Citation(s) |
29040764 |
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| Submission date |
Apr 26, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Pishun Li |
| E-mail(s) |
lipishun@hotmail.com
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| Phone |
9193164745
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| Organization name |
National Institute of Environmental Health Sciences
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| Department |
ESCBL
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| Lab |
stem cell
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| Street address |
111 T.W. Alexander Drive
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| City |
Research Triangle Park |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (2) |
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| This SubSeries is part of SuperSeries: |
| GSE98256 |
Rif1 Promotes a Repressive Chromatin State to Safeguard Against Endogenous Retrovirus Activation |
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| Relations |
| BioProject |
PRJNA384488 |
| SRA |
SRP105373 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE98254_RAW.tar |
1.7 Gb |
(http)(custom) |
TAR (of BEDGRAPH) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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