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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 13, 2014 |
| Title |
Localization of the Rb tumor suppressor in MEFs during reprogramming to iPS and the consequence of Rb loss on the transcriptional profile and histone landscape in these cells |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
The reprogramming of differentiated cells to an embryonic stem cell-like state provides a powerful system to explore fundamental mechanisms of development, including how mammalian cells establish and maintain pluripotency and long-term self-renewal capability. Based on the similarities between embryonic stem cells and cancer cells, we investigated the potential role of the retinoblastoma tumor suppressor and cell cycle regulator RB in the reprogramming of fibroblasts into induced pluripotent stem cells (iPS cells). Herein we demonstrate that loss of RB function leads to both an acceleration of the reprogramming process and the generation of more iPS clones from fibroblasts. This effect is largely due to a restrictive role for RB at the early stages of reprogramming. Surprisingly, however, RB inactivation does not enhance the formation of iPS clones by accelerating the proliferation of cells undergoing reprogramming. Rather, a genome-wide investigation of RB targets indicates that RB binds to regulatory regions of pluripotency genes such as Sox2 and Oct4 and contributes to their full repression in differentiated cells. This effect correlates with the maintenance of a repressive chromatin structure at these loci. Accordingly, Rb-deficient fibroblasts can be reprogrammed into iPS cells even in the absence of exogenous Sox2, which is normally required to initiate reprogramming from fibroblasts. These experiments identify a novel barrier in the reprogramming process, mainly the repression of certain pluripotency genes such as Sox2 by RB, which provides a new link between tumor suppressor mechanisms and cellular reprogramming.
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| Overall design |
RNAseq from MEFs with 2 biological replicates (save CP), Rb ChIPseq from MEFs with 2 biological replicates, Histone H3 modification ChIPseq from MEFs with 1 biological replicate
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| Contributor(s) |
Kareta MS, Gorges LL, Hafeez S, Spacek D, Batista LF, Vaka D, Artandi SE, Sage J, Wernig M |
| Citation(s) |
25467916 |
| Submission date |
Sep 04, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Julien Sage |
| E-mail(s) |
julsage@stanford.edu
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| Phone |
(650) 723-5113
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| Organization name |
Stanford University
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| Department |
Pediatrics
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| Lab |
Sage
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| Street address |
265 Campus Drive, SIM1 G2078
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305-5457 |
| Country |
USA |
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| Platforms (1) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (18)
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| GSM997573 |
GFP-infected cKO MEFs RNAseq |
| GSM997574 |
GFP-infected with 4F cKO MEFs RNAseq |
| GSM997575 |
Cre-infected cKO MEFs RNAseq biological replicate 2 |
| GSM997576 |
Cre-infected with 4F cKO MEFs RNAseq |
| GSM997577 |
GFP-infected cKO MEFs 10%TI ChIPseq |
| GSM997578 |
GFP-infected cKO MEFs RB ChIPseq |
| GSM997579 |
GFP-infected with 4F cKO MEFs 10%TI ChIPseq |
| GSM997580 |
GFP-infected with 4F cKO MEFs RB ChIPseq |
| GSM997581 |
GFP-infected cKO MEFs 10%TI histone ChIPseq biological replicate 1 |
| GSM997582 |
GFP-infected cKO MEFs H3Ac ChIPseq biological replicate 3 |
| GSM997583 |
GFP-infected cKO MEFs H3K4me3 ChIPseq biological replicate 3 |
| GSM997584 |
GFP-infected cKO MEFs H3K9me3 ChIPseq biological replicate 3 |
| GSM997585 |
GFP-infected cKO MEFs H3K27me3 ChIPseq biological replicate 3 |
| GSM997586 |
Cre-infected cKO MEFs 10%TI histone ChIPseq biological replicate 3 |
| GSM997587 |
Cre-infected cKO MEFs H3Ac ChIPseq biological replicate 3 |
| GSM997588 |
Cre-infected cKO MEFs H3K4me3 ChIPseq biological replicate 3 |
| GSM997589 |
Cre-infected cKO MEFs H3K9me3 ChIPseq biological replicate 3 |
| GSM997590 |
Cre-infected cKO MEFs H3K27me3 ChIPseq biological replicate 3 |
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| Relations |
| BioProject |
PRJNA174435 |
| SRA |
SRP015417 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE40594_RAW.tar |
74.0 Mb |
(http)(custom) |
TAR (of BED, WIG) |
| GSE40594_genes.fpkm_tracking.gz |
2.4 Mb |
(ftp)(http) |
FPKM_TRACKING |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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