GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE81899 Query DataSets for GSE81899
Status Public on Aug 30, 2017
Title OCT4 and SOX2 Work as Transcriptional Activators in Reprogramming Human Fibroblasts
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary SOX2 and OCT4, in conjunction with KLF4 and cMYC, are sufficient to reprogram human fibroblasts to induced pluripotent stem cells (iPSCs), but it is unclear if they function as transcriptional activators or as repressors. We now show that, like OCT4, SOX2 functions as a transcriptional activator. We substituted SOX2-VP16 (a strong activator) for wild-type (WT) SOX2, and we saw an increase in the efficiency and rate of reprogramming, whereas the SOX2-HP1 fusion (a strong repressor) eliminated reprogramming. We report that, at an early stage of reprogramming, virtually all DNA-bound OCT4, SOX2, and SOX2-VP16 were embedded in putative enhancers, about half of which were created de novo. Those associated with SOX2-VP16 were, on average, stronger than those bearing WT SOX2. Many newly created putative enhancers were transient, and many transcription factor locations on DNA changed as reprogramming progressed. These results are consistent with the idea that, during reprogramming, there is an intermediate state that is distinct from both parental cells and iPSCs
Overall design We ectopically expressed, in human fibroblasts, proteins comprising either a strong activating  (VP16) or a repressing region (HP1) fused to each of the factors- OCT4, SOX2, KLF4 and cMYC (OSKM).   SOX2-VP16, in combination with the WT forms of the other three proteins, uniquely increased the efficiency of reprogramming, especially of cells taken from older (37-96 year old) donors. The mix evoked early (by day 5), and strong, expression of critical pluripotency genes (e.g. NANOG), and diminished the requirement for cMYC . Many pre-existing ‘active’ enhancers were attenuated, and a smaller number of new enhancers, especially at sites of OCT4, SOX2 and SOX2-VP16 binding, were created by day 5.  The activities of new enhancers created by SOX2-VP16 binding were generally greater than those created by WT SOX2. Thus SOX2 and OCT4 work as activators capable of creating new enhancers, and increasing the activating function of SOX2 increases the activities of the new enhancers and the efficiencies of reprogramming.
Contributor(s) Narayan S, Shah S, Bryant GO, Ptashne M
Citation(s) 28813671
Submission date May 25, 2016
Last update date May 15, 2019
Contact name Mark Ptashne
Organization name Sloan Kettering Institute
Department Molecular Biology Program
Lab Mark Ptashne
Street address 1275 York Ave
City New York
State/province NY
ZIP/Postal code 10065
Country USA
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (84)
GSM2183731 MRC5_rep1_PolII
GSM2183732 MRC5_rep2_PolII
GSM2183733 OSKM_rep1_PolII
This SubSeries is part of SuperSeries:
GSE81900 OCT4 and SOX2 Work as Transcriptional Activators in Reprogramming Human Fibroblasts
BioProject PRJNA324089
SRA SRP075968

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
GSE81899_BEDGRAPHfiles.tar.gz 43.3 Mb (ftp)(http) TAR
GSE81899_BEDfiles.tar.gz 760.5 Mb (ftp)(http) TAR
GSE81899_ChIP-Endo_Protocol.pdf 103.1 Kb (ftp)(http) PDF
GSE81899_WIGfiles.tar.gz 124.7 Mb (ftp)(http) TAR
GSE81899_reprogramming_db.txt.gz 364.5 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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