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Series GSE41903 Query DataSets for GSE41903
Status Public on Dec 04, 2012
Title TRIM28 repression of retrotransposon-based enhancers is necessary to preserve transcriptional dynamics in embryonic stem cells
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary TRIM28 (KAP1 - KRAB-associated protein 1) is critical for the silencing of endogenous retroviruses (ERVs) in embryonic stem (ES) cells. Here, we reveal that an essential impact of this process is the protection of cellular gene expression in early embryos from perturbation by cis-acting activators contained within these genetic invaders. In TRIM28-depleted ES cells, repressive chromatin marks at ERVs are replaced by histone modifications typical of active enhancers, stimulating transcription of nearby cellular genes, notably those harboring bivalent promoters. Correspondingly, ERV-derived sequences can repress or enhance expression from an adjacent promoter in transgenic embryos depending on their TRIM28-sensitivity in ES cells. TRIM28-mediated control of ERVs is therefore crucial not just to prevent retrotransposition, but more broadly to safeguard the transcriptional dynamics of early embryos.
Overall design Analyses of transcriptional profiles and chromatin state in TRIM28 WT and KO cells
Contributor(s) Rowe HM, Kapopoulou A, Corsinotti A, Fasching L, Macfarlan TS, Tarabay Y, Viville S, Jakobsson J, Pfaff SL, Trono D
Citation(s) 23233547
Submission date Oct 29, 2012
Last update date May 15, 2019
Contact name Adamandia Kapopoulou
Phone 0041216930940
Organization name EPFL
Department Sciences de la Vie
Lab Trono
Street address Station 15
City Lausanne
ZIP/Postal code 1015
Country Switzerland
Platforms (2)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (18)
GSM1032182 mRNA-seq: ES KAP1 WT (ES3 cells)
GSM1032183 mRNA-seq: ES KAP1 KO (ES3 cells)
GSM1032184 mRNA-seq: MEF KAP1 WT
BioProject PRJNA179089
SRA SRP017085

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Supplementary file Size Download File type/resource
GSE41903_RAW.tar 880.0 Kb (http)(custom) TAR (of BED)
GSE41903_RefSeq_ES_rpkm_GEO.txt.gz 1.3 Mb (ftp)(http) TXT
GSE41903_RefSeq_MEF_rpkm_GEO.txt.gz 1.2 Mb (ftp)(http) TXT
GSE41903_Rex1GFP_KAP1_KD_GEO.xls.gz 556.5 Kb (ftp)(http) XLS
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Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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