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Series GSE130416 Query DataSets for GSE130416
Status Public on Apr 30, 2019
Title Hominid-specific transposable elements and KRAB-ZFPs facilitate human embryonic genome activation and transcription in naïve hESCs [RNA-seq]
Organism Homo sapiens
Experiment type Expression 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 RNA-seq was performed in WIBR3dPE hESC in KN/2iL media or in Induced Neurons upon dCAS9-KRAB overexpression containing or not a guide RNA targeting LTR7YB or SVA/LTR5Hs or overexpressing ZNF611; in H1 primed hESC overexpressing GFP, KLF4 or KLF17
 
Contributor(s) Duc J, Pontis J
Citation(s) 31006620
Submission date Apr 29, 2019
Last update date May 01, 2019
Contact name Julien Duc
E-mail(s) julien.duc@epfl.ch
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 (34)
GSM3738296 RNA-seq_naive_hESC+dCAS9-KRAB_without_sgLTR7YB_rep1
GSM3738297 RNA-seq_naive_hESC+dCAS9-KRAB_without_sgLTR7YB_rep2
GSM3738298 RNA-seq_naive_hESC+dCAS9-KRAB_sgLTR7YB_A_rep1
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 PRJNA540219
SRA SRP194102

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

Supplementary file Size Download File type/resource
GSE130416_RAW.tar 53.3 Mb (http)(custom) TAR (of TAB)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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