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Series GSE130418 Query DataSets for GSE130418
Status Public on Apr 30, 2019
Title Hominid-specific transposable elements and KRAB-ZFPs facilitate human embryonic genome activation and transcription in naïve hESCs [ATAC-seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Transposable elements (TEs) are key to the evolutionary turnover of regulatory sequences. How they can play such an essential role in spite of their genotoxic potential is unknown. Here, we demonstrate that KRABcontaining zinc finger proteins control the timely and pleiotropic engagement of TE-derived cis-regulators of transcription. We first observed that evolutionary recent TEs of the SVA, HERVK and HERVH subgroups are major contributors to chromatin opening during human embryonic genome activation and act as KLF-stimulated enhancers in naïve embryonic stem cells. We then found that KZFPs of corresponding evolutionary ages are simultaneously induced and repress the transcriptional activity of these TEs. We finally determined that the same KZFP-controlled TE-based enhancers later serve as developmental and tissue-specific regulators of gene expression. Thus, by taming the transcriptional impact of TEs during early embryogenesis, KZFPs allow for their genome-wide incorporation into transcriptional networks, thereby contributing to the species-specificity of human genome regulation.
 
Overall design ATAC-seq was performed on primed WIRB3 and WIBR3dPE; naïve WIBR3 and WIBR3dPE in 4iLA and KN/2iL media respectively; and in WIBR3dPE in KN/2iL media upon dCAS9-KRAB overexpression containing or not a guide RNA targeting SVA/LTR5Hs
 
Contributor(s) Duc J, Pontis J
Citation(s) 31006620
Submission date Apr 29, 2019
Last update date Jan 05, 2021
Contact name Julien Duc
E-mail(s) [email protected]
Organization name EPFL
Department School of Life Science
Lab LVG
Street address Station 19 CH-1015 Lausanne
City Lausanne
State/province VAUD
ZIP/Postal code 1015
Country Switzerland
 
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (10)
GSM3738369 ATAC-seq_naive_hESC_dCAS9-KRAB_Empty_rep1
GSM3738370 ATAC-seq_naive_hESC_dCAS9-KRAB+sgRNA_rep1
GSM3738371 ATAC-seq_naive_hESC_dCAS9-KRAB_Empty_rep2
This SubSeries is part of SuperSeries:
GSE117395 Hominid-specific transposable elements and KRAB-ZFPs facilitate human embryonic genome activation and transcription in naïve hESCs
Relations
BioProject PRJNA540225
SRA SRP194104

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE130418_RAW.tar 25.0 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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