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| Status |
Public on Feb 14, 2019 |
| Title |
Construction of a dynamic gene regulatory network required for cellular reprogramming |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by array
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
The generation of induced Pluripotent Stem Cells (iPSCs) from somatic cells provides an excellent example to study mechanisms of transcription factor-induced global alterations of the genome and the epigenome. Here, we have investigated the early transcriptional events of cellular reprogramming triggered by the co-expression of OSKM (Oct4, Sox2, Klf4 and c-Myc) in Mouse Embryonic Fibroblasts (MEFs) and mouse Hepatocytes (mHeps) and identified a novel gene regulatory network composed of 9 Transcriptional Regulators (TRs), which are directly targeted by OSKM. Functional studies using single and double shRNA knock-downs of any of these TRs caused disruption of the network and dramatic reductions in reprogramming efficiency, demonstrating that this novel gene regulatory network is essential for the induction and establishment of pluripotency. We demonstrate that that the stochastic co-expression of the 9TRs network components occurs in a remarkably small number of cells approximating the percentage of reprogrammed cells as the result of dynamic molecular events. Thus, the early binding patterns of OSKM and the subsequent stochastic co-expression of pivotal TRs in subpopulations of cells steer the reconstruction of a gene regulatory network crucial for the generation of iPSCs.
In this study, we show that OSKM trigger the gradual establishment of the stemness phenotype by inducing the stochastic reconstruction of a novel 9TRs gene regulatory network that guides the acquisition to pluripotency.
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| Overall design |
Affymetrix Mouse Genome 430 A 2.0 version was used for gene expression profiling of the reprogramming course. RNA was isolated from mESCs, miPSCs, control (naïve) MEFs and reprogrammable MEFs on day 0.5, 1, 1.5, 2, 2.5, 3, 6, 12, 18 of reprogramming. Additional RNA was isolated from mHeps at days 0, 3 and 6 of reprogramming.
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| Contributor(s) |
Thanos D, Polyzos A |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
May 17, 2018 |
| Last update date |
Sep 28, 2020 |
| Contact name |
Prokopios Alexandros Polyzos |
| E-mail(s) |
app2006@med.cornell.edu
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| Organization name |
Weill Cornell Medicine
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| Street address |
413 E 69th St
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| City |
New York |
| ZIP/Postal code |
10021 |
| Country |
USA |
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| Platforms (3) |
| GPL8321 |
[Mouse430A_2] Affymetrix Mouse Genome 430A 2.0 Array |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (55)
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| Relations |
| BioProject |
PRJNA471847 |
| SRA |
SRP271458 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE114581_RAW.tar |
43.8 Mb |
(http)(custom) |
TAR (of BED, CEL) |
SRA Run Selector |
| Raw data provided as supplementary file |
| Processed data included within Sample table |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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