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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 01, 2016 |
| Title |
Chromatin decompaction coupled MuERVL endogenous retrovirus activation induces genome-wide DNA demethylation |
| Organism |
Mus musculus |
| Experiment type |
Methylation profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Mouse embryonic stem cells are heterogeneous and contain rare cells expressing transcripts normally upregulated in pre-implantation embryos, including the Zscan4 cluster and MuERVL endogenous retrovirus. Through single cell transcriptomics and genome-wide chromatin and DNA methylation analyses we uncover the dynamics of the regulation and epigenetic consequences of these transient cells. Transcriptional activation of MuERVL and Zscan4 coincided with a global increase in chromatin accessibility. Through a combination of bulk and single-cell RNA-sequencing, we reveal the dynamics and specificities of a MuERVL driven transcriptional network. Interestingly, in addition to pre-implantation embryos, the MuERVL network is similarly upregulated during somatic cell reprogramming, associating it with dramatic chromatin remodeling events. In MuERVL+ mESCs, upregulation of a cluster of Eif1A-like genes results in inhibition of protein synthesis, uncoupling transcription from translation. Consequently, depletion of proteins including DNA methyltransferases, results in genome-wide DNA demethylation, demonstrating the influence of endogenous retroviral activation on the host epigenome.
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| Overall design |
Total RNA-seq libraires (3 biological replicates of 2 samples, 4 biological replicates of a third sample); ATAC-seq (4 biological replicates of 3 samples each); Bisulfite-seq (3 biological replicates of 2 samples)
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| Contributor(s) |
Eckersley-Maslin MA, Svensson V, Krueger C, Giehr P, Milagre I, Miragaia R, Stubbs T, Krueger F, Walter J, Teichmann S, Reik W |
| Citation(s) |
27681430 |
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| Submission date |
Dec 07, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Felix Krueger |
| E-mail(s) |
[email protected]
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| Organization name |
Altos Labs
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| Department |
Bioinformatics
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| Street address |
Granta Park
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| City |
Cambridge |
| ZIP/Postal code |
CB21 6GP |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (25)
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| Relations |
| BioProject |
PRJNA305313 |
| SRA |
SRP067094 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE75751_ATAC-Seq.500bp_tile_report.txt.gz |
123.2 Mb |
(ftp)(http) |
TXT |
| GSE75751_RAW.tar |
1.0 Gb |
(http)(custom) |
TAR (of TXT) |
| GSE75751_Ribominus_RNA-Seq_probe_report.txt.gz |
1.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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