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| Status |
Public on Mar 15, 2016 |
| Title |
Transposable elements and their KRAB-ZFP controllers regulate gene expression in adult tissues |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
The tetrapod-restricted KRAB-containing zinc finger proteins (KRAB-ZFPs) are essential early embryonic controllers of transposable elements (TEs), which they repress via their cofactor KAP1 and associated effectors through histone and DNA methylation, a process thought to result in irreversible silencing. Using a target-centered functional screen, we matched several murine TEs with their cognate KRAB-ZFP. This revealed an unexpected level of granularity in their interactions, with KRAB-ZFPs recognizing TEs from more than one subfamily, TEs recruiting more than one KRAB-ZFP, and spatially and temporally differential KRAB-ZFP-mediated regulation of TEs and nearby genes. Most importantly, we discovered that the KRAB/KAP1 system controls TEs in adult tissues, in cell culture and in vivo, where they partner up to regulate the expression of cellular genes. Therefore, TEs and KRAB-ZFPs establish widely active transcription networks that regulate not only development but probably also many physiological events. Given the high degree of species-specificity of both TEs and KRAB-ZFPs, these results have important implications for studying and understanding the biology of higher vertebrates, including humans.
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| Overall design |
Analysis of transcriptional profiles of KAP1 or ZFP932/Gm15446 KO cells or tissues, and ZFP932 and Gm15446 ChIPseq in murine ES and C2C12 cells.
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| Contributor(s) |
Ecco G, Cassano M, Kauzlaric A, Duc J, Trono D |
| Citation(s) |
27003935 |
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| Submission date |
Oct 22, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Julien Duc |
| E-mail(s) |
julien.duc@epfl.ch
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| Organization name |
EPFL
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| Department |
School of Life Science
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| Lab |
LVG
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| Street address |
Station 19 CH-1015 Lausanne
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| City |
Lausanne |
| State/province |
VAUD |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
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| Platforms (1) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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| Samples (41)
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| Relations |
| BioProject |
PRJNA299625 |
| SRA |
SRP065215 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE74278_RAW.tar |
6.9 Gb |
(http)(custom) |
TAR (of BED, BW, TXT) |
| GSE74278_experiment.xml.gz |
3.2 Kb |
(ftp)(http) |
XML |
| GSE74278_run.xml.gz |
2.1 Kb |
(ftp)(http) |
XML |
| GSE74278_submission.xml.gz |
516 b |
(ftp)(http) |
XML |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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