GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE56567 Query DataSets for GSE56567
Status Public on Aug 04, 2014
Title Critical role of transient activation of human endogenous retroviruses during reprogramming toward pluripotency (Chip-Seq)
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary We recently showed that some human induced pluripotent stem cell (iPSC) clones were defective in neural differentiation and were marked with the activation of long term repeats (LTRs) of human endogenous retroviruses (HERVs). We herein demonstrated that these LTRs were transiently overexpressed during the generation of iPSCs and contributed to reprogramming. When the generation of iPSCs was completed, LTRs were re-suppressed to levels similar to those in human ES cells. However, differentiation-defective iPSC clones maintained high LTR expression levels, which indicated that these clones failed to complete reprogramming. lincRNA-RoR, a long intergenic non-coding RNA (lincRNA) that was previously shown to support the induction and maintenance of pluripotency, was detected among the LTR-driven transcripts. Short hairpin RNAs against the conserved sequence in LTRs or lincRNA-RoR markedly reduced the efficiency of iPSC generation. Reprogramming factors including OCT3/4, SOX2, and KLF4 bound to most LTRs. The expression of KLF4 was low in normal iPSC clones, but remained high in differentiation-defective clones. The forced expression of KLF4 in human embryonic stem cells led to the activation of LTRs and defects in neural differentiation. These results demonstrated that the transient overexpression of KLF4/LTR/lincRNA-RoR played crucial roles in reprogramming toward pluripotency in humans, whereas a failure in its re-silence resulted in differentiation defects.
Overall design OCT3/4, SOX2 and KLF4 bindings in human dermal fibroblast and iPSC
Contributor(s) Ohnuki M, Watanabe A, Takahashi K
Citation(s) 25097266
Submission date Apr 07, 2014
Last update date May 15, 2019
Contact name Akira Watanabe
Organization name Kyoto University
Department Medical Innovation Center
Street address Shogoin-Kawahara-cho 53, Sakyo-ku
City Kyoto
State/province Kyoto
ZIP/Postal code 606-8507
Country Japan
Platforms (3)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (8)
GSM1364022 Of-S-K-M
GSM1364023 O-Sf-K-M
GSM1364024 O-S-Kf-M
This SubSeries is part of SuperSeries:
GSE56569 Critical role of transient activation of human endogenous retroviruses during reprogramming toward pluripotency
BioProject PRJNA243928
SRA SRP041007

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
GSE56567_RAW.tar 5.1 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap