PP003
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
SUBMITTER: Marian Groot Koerkamp
PROVIDER: E-TABM-1218 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
A central role for TFIID in the pluripotent transcription circuitry.
Pijnappel W W M Pim WW Esch Daniel D Baltissen Marijke P A MP Wu Guangming G Mischerikow Nikolai N Bergsma Atze J AJ van der Wal Erik E Han Dong Wook DW Bruch Hermann vom Hv Moritz Sören S Lijnzaad Phillip P Altelaar A F Maarten AF Sameith Katrin K Zaehres Holm H Heck Albert J R AJ Holstege Frank C P FC Schöler Hans R HR Timmers H T Marc HT
Nature 20130317 7442
Embryonic stem (ES) cells are pluripotent and characterized by open chromatin and high transcription levels, achieved through auto-regulatory and feed-forward transcription factor loops. ES-cell identity is maintained by a core of factors including Oct4 (also known as Pou5f1), Sox2, Klf4, c-Myc (OSKM) and Nanog, and forced expression of the OSKM factors can reprogram somatic cells into induced pluripotent stem cells (iPSCs) resembling ES cells. These gene-specific factors for RNA-polymerase-II-m ...[more]
Similar Datasets
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2013-03-21 | E-GEOD-33646 | biostudies-arrayexpress
Project description:Pluripotent stem cells can be isolated from early embryos or induced by cell fusion, somatic nuclear transfer, or expression of a selected set of transcription factors. Embryonic stem (ES) cells are characterized by an open chromatin configuration and high transcription levels achieved via autoregulatory and feed-forward transcription factor loops. How the general transcription machinery is involved in pluripotency is unclear. Here, we show that TFIID knockdown affected the pluripotent circuitry in ES cells and inhibited reprogramming of fibroblasts. TFIID and pluripotency factors form a feed-forward loop to induce and maintain a stable transcription state. Strikingly, transient expression of TFIID subunits greatly enhanced reprogramming by Oct4, Sox2, Klf4 and c-Myc reaching efficiencies upto 50%. These results show that TFIID is a critical and selective component for transcription factor-mediated reprogramming. We anticipate that by creating plasticity in gene expression programs, basal transcription complexes such as TFIID assist reprogramming into different cellular states. Three iPS lines, iPS#1, iPS#4, and iPS#5 were used in duplicate for microarray analysis against a pool of RNA from ES-cells.
2013-03-21 | E-GEOD-33645 | biostudies-arrayexpress
Project description:Pluripotency can be induced in murine and human fibroblast by transduction of four transcription factors (Oct4, Sox2, Klf4 and c-Myc). Previously we reported that two factors (Oct4 and Klf4) are sufficient for reprogramming adult mouse neural stem cells (NSCs) to a pluripotent state. However, although NSCs endogenously express the factors Sox2, c-Myc, and Klf4, our previous report does not elucidate why exogenous expression of either Klf4 or c-Myc is still required for reprogramming. Here we report that exogenous expression of Oct4 is sufficient to generate one-factor induced pluripotent stem (1F iPS) cells without any oncogenic factors, such as c-Myc and Klf4, from mouse adult NSCs, which endogenously express Sox2, c-Myc, and Klf4, and also intermediate reprogramming markers alkaline phosphatase (AP), stage-specific embryonic antigen-1 (SSEA-1). These results extend our previous report proposing that somatic cells can be reprogrammed to a pluripotent state with a reducing number of reprogramming factors when the complementing factors are endogenously expressed in the somatic cells. Experiment Overall Design: 10 hybridizations in total. Experiment Overall Design: NSC-derived iPS cells by one-factor (Oct4) in triplicate: Experiment Overall Design: - NSC_1F_iPS_1 Experiment Overall Design: - NSC_1F_iPS_2 Experiment Overall Design: - NSC_1F_iPS_3 Experiment Overall Design: One-factor (Oct4) iPS cell-derived NSC in triplicate: Experiment Overall Design: - 1F_iPS_NSC_1 Experiment Overall Design: - 1F_iPS_NSC_2 Experiment Overall Design: - 1F_iPS_NSC_3 Experiment Overall Design: Neural stem cell (NSC) derived from brain of OG2/Rosa26 mice: Experiment Overall Design: - NSC_1 Experiment Overall Design: - NSC_2 Experiment Overall Design: - NSC_3 Experiment Overall Design: - NSC_4
2009-02-08 | E-GEOD-12499 | biostudies-arrayexpress
Project description:Reactivation of the pluripotency network during somatic cell reprogramming by exogenous transcription factors involves chromatin remodeling and the recruitment of RNA polymerase II (Pol II) to target loci. Here, we report that Pol II is engaged at pluripotency promoters in reprogramming but remains paused and inefficiently released. We also show that bromodomain-containing protein 4 (BRD4) stimulates productive transcriptional elongation of pluripotency genes by dissociating the pause release factor P-TEFb from an inactive complex containing HEXIM1. Consequently, BRD4 overexpression enhances reprogramming efficiency and HEXIM1 suppresses it, whereas Brd4 and Hexim1 knockdown do the opposite. We further demonstrate that the reprogramming factor KLF4 helps recruit P-TEFb to pluripotency promoters. Our work thus provides a mechanism for explaining the reactivation of pluripotency genes in reprogramming and unveils an unanticipated role for KLF4 in transcriptional pause release. Pol II ChIP-seq for MEFs, ESCs and bulk populations of OSKM reprogramming intermediates at two time points.
2014-10-07 | E-GEOD-59828 | biostudies-arrayexpress
Project description:Reactivation of the pluripotency network during somatic cell reprogramming by exogenous transcription factors involves chromatin remodeling and the recruitment of RNA polymerase II (Pol II) to target loci. Here, we report that Pol II is engaged at pluripotency promoters in reprogramming but remains paused and inefficiently released. We also show that bromodomain-containing protein 4 (BRD4) stimulates productive transcriptional elongation of pluripotency genes by dissociating the pause release factor P-TEFb from an inactive complex containing HEXIM1. Consequently, BRD4 overexpression enhances reprogramming efficiency and HEXIM1 suppresses it, whereas Brd4 and Hexim1 knockdown do the opposite. We further demonstrate that the reprogramming factor KLF4 helps recruit P-TEFb to pluripotency promoters. Our work thus provides a mechanism for explaining the reactivation of pluripotency genes in reprogramming and unveils an unanticipated role for KLF4 in transcriptional pause release. Refer to individual Series
2014-10-07 | E-GEOD-59833 | biostudies-arrayexpress
Project description:Reprogramming of somatic cells is a valuable tool to understand the mechanisms of regaining pluripotency and further opens up the possibility to generate patient-specific pluripotent stem cells. Reprogramming of mouse and human somatic cells into pluripotent stem cells, designated as induced pluripotent stem (iPS) cells, has been possible with the expression of the transcription factor quartet Oct4, Sox2, c-Myc, and Klf4. Considering that ectopic expression of c-Myc causes tumourigenicity in offspring and retroviruses themselves can cause insertional mutagenesis, the generation of iPS cells with a minimal number of factors may hasten the clinical application of this approach. Here, we show that adult mouse neural stem cells (NSCs) express higher endogenous levels of Sox2 and c-Myc than ES cells and that exogenous Oct4 together with either Klf4 or c-Myc are sufficient to generate iPS cells from NSCs. These two-factor (2F) iPS cells are similar to embryonic stem cells at the molecular level, contribute to development of the germline, and form chimeras. We propose that, in inducing pluripotency, the number of reprogramming factors can be reduced when using somatic cells that endogenously express appropriate levels of complementing factors. Experiment Overall Design: 8 hybridizations in total. Experiment Overall Design: NSC derived iPS cells by 2 factors (Oct4 and Klf4) in triplicate: Experiment Overall Design: - iPS cell_2F_1 Experiment Overall Design: - iPS cell_2F_2 Experiment Overall Design: - iPS cell_2F_3 Experiment Overall Design: Embryonic Stem cells (ESC) in triplicate: Experiment Overall Design: - ESC_1 Experiment Overall Design: - ESC_2 Experiment Overall Design: - ESC_3 Experiment Overall Design: NSC cultures in duplicates: Experiment Overall Design: - NSC_2 Experiment Overall Design: - NSC_3 Experiment Overall Design: NSC derived iPS cells by 4 factors (Oct4, Sox2, c-Myc and Klf4) in triplicate: Experiment Overall Design: - iPS cell_4F_1 Experiment Overall Design: - iPS cell_4F_2 Experiment Overall Design: - iPS cell_4F_3
2008-10-20 | E-GEOD-10806 | biostudies-arrayexpress
Project description:Co-activator complexes regulate chromatin accessibility and transcription. SAGA (Spt-Ada-Gcn5 Acetyltransferase) is an evolutionary conserved multisubunit co-activator complex with modular organization. The core module of SAGA constitutes the structural heart, composed of a histone octamer like structure and two additional proteins. The central histone octamer like core structure consists of six histone fold domain (HFD)-containing proteins, forming three HF pairs (TADA1/TAF12, TAF6L/TAF9/9b, and TAF10/SUPT7L) in the mammalian SAGA complexes, to which adds SUPT3H, which contains an intramolecular HF pair. The yeast homologue of SUPT3H, called Spt3, was shown to interact genetically and biochemically with the TATA binding protein (TBP). Here we investigated the role of SUPT3H in human U2OS and mouse embryonic stem (ES) cells. Using immuno-purification coupled mass spectrometry experiments we show that both human and mouse SAGA can assemble without the double HFD-containing SUPT3H. Nascent RNA-seq experiments indicted that in either U2OS or mouse ESCs lacking SUPT3H only a small subset of genes is deregulated. Consequently, in mouse ESCs SUPT3H is not essential for mouse ESC survival, but is required for ESC growth and self-renewal. In addition, TBP recruitment experiments show no major change in TBP accumulation at gene promoters in the absence of SUPT3H in mouse and human cells. Taken together our data suggest in mammalian cells SUPT3H is not required for the assembly of SAGA, general TBP recruitment to genes and cell survival, but it is important for regulating a limited set of genes.
2022-07-26 | PXD026991 | Pride
Project description:SAGA and ATAC are two related transcriptional coactivator complexes, sharing the same histone acetyltransferase (HAT) subunit. The HAT activities of SAGA and ATAC are required for metazoan development but the precise role of the two complexes in RNA polymerase II transcription in mammals is less understood. To determine whether SAGA and ATAC have redundant or specific functions dependent on their HAT activities, we compared the effects of HAT inactivation in each complex with that of inactivation of either SAGA or ATAC core subunits in mouse embryonic stem cells (ESCs). We show that core subunits of SAGA or ATAC subunits are required for complex assembly, mouse ESC growth and self-renewal. Additionally, ATAC, but not SAGA subunits are required for ESC viability by regulating the transcription of translation-related genes. Surprisingly, depletion of specific or shared HAT module subunits caused a global decrease in histone H3K9 acetylation, but did not result in significant phenotypic or transcriptional defects. Thus, our results indicate that SAGA and ATAC are differentially required for viability and self-renewal of mouse ESCs by regulating transcription through different pathways, in a HAT-independent manner.
2021-08-11 | PXD027026 | Pride
Project description:Groundbreaking work demonstrated that ectopic expression of four transcription factors, Oct4, Klf4, Sox2, and c-Myc, could reprogram murine somatic cells to induced pluripotent stem cells (iPSCs) (Takahashi and Yamanaka, 2006), and human iPSCs were subsequently generated using similar genetic manipulation (Takahashi et al., 2007,Yu et al., 2007). To address the safety issues arose from harboring integrated exogenous sequences in the target cell genome, a number of modified genetic methods have been developed and produced iPSCs with potentially reduced risks (for discussion, see Yamanaka, 2009, and references therein). However, all of the methods developed to date still involve the use of genetic materials and thus the potential for unexpected genetic modifications by the exogenous sequences in the target cells. Here we report generation of protein-induced pluripotent stem cells (piPSCs) from murine embryonic fibroblasts using recombinant cell-penetrating reprogramming proteins. We demonstrated that such piPSCs can long-term self-renew and are pluripotent in vitro and in vivo. Global gene-expression analyses of the piPS cells
2010-04-09 | E-GEOD-16062 | biostudies-arrayexpress
Project description:Recent studies demonstrated that fibroblasts could be converted into induced neural stem cells (iNSCs). However, the insertional mutation caused by random integration of viral vectors has been a major limitation of iNSCs for the future clinical translation. Here we show that non-viral transfection of episomal vectors encoding Brn4/Pou3f4, Sox2, Klf4, and c-Myc sufficiently generates iNSCs. The episomal vector mediated iNSCs closely resemble brain-derived NSCs as well as iNSCs generated by retrovirus in morphology, gene expression profile, epigenetic status, self-renewal capacity and both in vitro and in vivo differentiation capacity. The novel conversion protocol defined in the current study offers a method for generating integration-free iNSCs for the clinical research we developed a novel method for generating integration-free iNSCs. We demonstrated that oriP/EBNA1-based episomal vectors could generate iNSCs by single transfection
2015-03-27 | E-GEOD-67319 | biostudies-arrayexpress