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| 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
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| 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
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| 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.
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| Contributor(s) |
Narayan S, Shah S, Bryant GO, Ptashne M |
| Citation(s) |
28813671 |
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| Submission date |
May 25, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Mark Ptashne |
| E-mail(s) |
m-ptashne@mskcc.org
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| Organization name |
Sloan Kettering Institute
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| Department |
Molecular Biology Program
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| Lab |
Mark Ptashne
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| Street address |
1275 York Ave
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (84)
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| This SubSeries is part of SuperSeries: |
| GSE81900 |
OCT4 and SOX2 Work as Transcriptional Activators in Reprogramming Human Fibroblasts |
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| Relations |
| BioProject |
PRJNA324089 |
| SRA |
SRP075968 |
| 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 Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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