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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Pluripotency transcription factor Oct4 mediates stepwise nucleosome demethylation and depletion

ABSTRACT: The mechanisms whereby the crucial pluripotency transcription factor Oct4 regulates target gene expression are incompletely understood. Using an assay system based on partially differentiated embryonic stem cells, we show that Oct4 opposes accumulation of local H3K9me2, and subsequent Dnmt3a-mediated DNA methylation. Upon binding DNA, Oct4 recruits the histone lysine demethylase Jmjd1c. ChIP timecourse experiments identify a stepwise Oct4 mechanism involving Jmjd1c recruitment and H3K9me2 demethylation, transient FACT complex recruitment, and nucleosome depletion. Genome-wide and targeted ChIP confirms binding of newly-synthesized Oct4, together with Jmjd1c and FACT, to the Pou5f1 enhancer and a small number of other Oct4 targets, including the Nanog promoter. Histone demethylation is required for both FACT recruitment and H3 depletion. Jmjd1c is required to induce endogenous Oct4 expression and fully reprogram fibroblasts to pluripotency, indicating that the assay system identifies functional Oct4 cofactors. These findings indicate that Oct4 sequentially recruits activities that catalyze histone demethylation and depletion. Examination of transcription factor occupancy in cells with newly synthesized Oct4.

ORGANISM(S): Mus musculus

SUBMITTER: Dean Tantin

PROVIDER: E-GEOD-65192 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Pluripotency transcription factor Oct4 mediates stepwise nucleosome demethylation and depletion

Project description:The mechanisms whereby the crucial pluripotency transcription factor Oct4 regulates target gene expression are incompletely understood. Using an assay system based on partially differentiated embryonic stem cells, we show that Oct4 opposes accumulation of local H3K9me2, and subsequent Dnmt3a-mediated DNA methylation. Upon binding DNA, Oct4 recruits the histone lysine demethylase Jmjd1c. ChIP timecourse experiments identify a stepwise Oct4 mechanism involving Jmjd1c recruitment and H3K9me2 demethylation, transient FACT complex recruitment, and nucleosome depletion. Genome-wide and targeted ChIP confirms binding of newly-synthesized Oct4, together with Jmjd1c and FACT, to the Pou5f1 enhancer and a small number of other Oct4 targets, including the Nanog promoter. Histone demethylation is required for both FACT recruitment and H3 depletion. Jmjd1c is required to induce endogenous Oct4 expression and fully reprogram fibroblasts to pluripotency, indicating that the assay system identifies functional Oct4 cofactors. These findings indicate that Oct4 sequentially recruits activities that catalyze histone demethylation and depletion.

2015-01-23 | GSE65192 | GEO

Chemical Inhibition of the RORγt-dependent Transcriptional Network in Th17 cells [ChIP-Seq]

Project description:RORγt is a transcription factor required for T helper 17 (Th17) cell development. We identified three RORγt-specific inhibitors that suppress Th17 cell responses including Th17 cell-mediated autoimmune disease. We systemically characterized RORγt binding data in the presence and absence of drug with corresponding whole-transcriptome sequencing for wild-type and RORγt-deficient cells. RORγt is central in a densely interconnected regulatory network, acting both as a direct activator of genes important for Th17 cell differentiation and as a direct repressor of genes from other T-cell lineages. The three inhibitors identified here reversed both of these modes of action, but to varying extents and through distinct mechanisms. Whereas one inhibitor displaced RORγt from its target-loci, the two more potent inhibitors affected transcription predominantly without removing DNA-binding. Our work illustrates the power of a system-scale analysis of transcriptional regulation to characterize potential therapeutic compounds that inhibit pathogenic Th17 cells and suppress autoimmunity. DNA binding of RORγt in WT Th17 cells and under chemical perturbations of RORγt; Additional data is included for epitope-tagged exogenous RORγt in EL4 cells (a murine lymphoma cell line)

2014-04-17 | E-GEOD-56019 | biostudies-arrayexpress

Genome-wide maps of O-GlcNAc-Oct4 binding regions in ZHBTc4 F-Oct4 mouse embryonic stem cells

Project description:We report that Oct4 is modified by O-GlcNAc in stem cells. To find O-GlcNAc-Oct4 target genes, we ChIPed Oct4 with Flag(Oct4) antibody and then O-GlcNAc modified proteins are enriched by sWGA beads (succinylated wheat germ agglutinin (sWGA), which specifically binds O-GlcNAc). Results show that several genes implicated in pluripotency regulation are bound by O-GlcNAc-Oct4 in their gene region. 2 samples examined: Control (ChIP with anti-Flag(Oct4) and then reChIP with IgG), O-GlcNAc-Oct4 (ChIP with anti-Flag (Oct4) and then reChIP with sWGA)

2012-08-27 | E-GEOD-36388 | biostudies-arrayexpress

Genome-wide maps of Sox/Oct partnerships pluripotent and lineage-committed cells

Project description:We show here by using genome-wide ChIP-sequencing that lineage segregation involves multiple Sox/Oct partnership. In undifferentiated ES cells Oct4 interacts with Sox2 and both TFs bind on the 'canonical' motif, whereas in cells commited to PrE lineage Oct4 switches from Sox2 to Sox17 interaction and this complex bind to a unique "compressed" motif. ChIP-sequencing has been done for Sox2, Sox17 and Oct4 in the pluripotent context or PrE context

2013-04-23 | E-GEOD-43275 | biostudies-arrayexpress

Genome-wide Oct4 binding profile in lung cancer A549 cells

Project description:Oct4 stemness gene encoding a transcription factor has been shown to overexpress in cancers. However, precise mechanisms of Oct4 relevant to transcriptional reprogramming leading to somatic cancer progression remain unclear. To address the Oct4-mediated transcriptional program in lung cancer, we integrated genome-wide Oct4 binding profiles from chromatin-immunoprecipitation sequencing and ENCODE datasets. We identified that Oct4 occupied at functional promoter and enhancer regions of genes which play key roles in several signaling pathways involving tumorigenesis. Genome-wide Oct4 binding sites were identified via chromatin immunoprecipitation-sequencing analysis of vecoter control and stably Oct4-overexpressing A549 lung cancer cells. ChIP-seq analyses were performed in duplicated samples using Applied Biosystems SOLiD system.

2015-02-04 | E-GEOD-58462 | biostudies-arrayexpress

OCT4, NANOG and CTCF in human embryonic stem cells

Project description:This SuperSeries is composed of the following subset Series: GSE20650: Genome-wide mapping of OCT4, NANOG and CTCF in human embryonic stem cells GSE21135: OCT4 Knockdown in human embryonic stem cells Refer to individual Series

2010-04-04 | E-GEOD-21200 | biostudies-arrayexpress

Genome-wide maps of chromatin remodeler SNF5 in human pluripotent cells.

Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of SNF5 binding in human pluripotent embryonic carcinoma NCCIT and SNF5 overexpressed NCCIT cells. We generated genome-wide cSNF5 maps of NCCIT and SNF5 overexpressed NCCIT cells from chromatin immunoprecipitated DNA. SNF5 and OCT4 seem not to share their binding in OCT4 centered binding plot in control, while SNF5 overexpression directs SNF5 to OCT4 target genes. Examination of the relationship between SNF5 and OCT4 binding in control and SNF5 overexpressed cells.

2013-01-01 | E-GEOD-36134 | biostudies-arrayexpress

Novel Foxo1-dependent Transcriptional Programs Control Treg Cell Function [ChIP-Seq]

Project description:Regulatory T (Treg) cells characterized by expression of the transcription factor forkhead box P3 (Foxp3) maintain immune homeostasis by suppressing self-destructive immune responses1-4. Foxp3 operates as a late acting differentiation factor controlling Treg cell homeostasis and function5, whereas the early Treg cell lineage commitment is regulated by the Akt kinase and the forkhead box O (Foxo) family of transcription factors6-10. However, whether Foxo proteins act beyond the Treg cell commitment stage to control Treg cell homeostasis and function remains largely unexplored. Here we show that Foxo1 is a pivotal regulator of Treg cell function. Treg cells express high amounts of Foxo1, and display reduced T-cell receptor-induced Akt activation, Foxo1 phosphorylation, and Foxo1 nuclear exclusion. Mice with Treg cell-specific deletion of Foxo1 develop a fatal inflammatory disorder similar in severity to Foxp3-deficient mice, but without the loss of Treg cells. Genome-wide analysis of Foxo1 binding sites reveals ~300 Foxo1-bound target genes, including the proinflammatory cytokine Ifng, that do not appear to be directly regulated by Foxp3. These findings demonstrate that the evolutionarily ancient Akt-Foxo1 signaling module controls a novel genetic program indispensable for Treg cell function. Treg cells were isolated from wild-type B6 mice or Foxo1tagBirA mice in which foxo1 is endogenously biotinylated. Foxo1 binding targets in Treg cells were identified by using Foxo1 antibody- and Streptavidin- ChIP-Seq approaches.

2012-09-07 | E-GEOD-40656 | biostudies-arrayexpress

Base-resolution methylation patterns accurately predict transcription factor bindings in vivo

Project description:Detecting in vivo transcription factor (TF) binding is important for understanding gene regulatory circuitries. ChIP-seq is a powerful technique to empirically define TF binding in vivo. However, the multitude of distinct TFs makes genome-wide profiling for them all labor-intensive and costly. Algorithms for in silico prediction of TF binding have been developed, based mostly on histone modification or DNase I hypersensitivity data in conjunction with DNA motif and other genomic features. However, technical limitations of these methods prevent them from being applied broadly, especially in clinical settings. We conducted a comprehensive survey involving multiple cell lines, TFs, and methylation types and found that there are intimate relationships between TF binding and methylation level changes around the binding sites. Exploiting the connection between DNA methylation and TF binding, we proposed a novel supervised learning approach to predict TF-DNA interaction using data from base-resolution whole-genome methylation sequencing experiments. We devised beta-binomial models to characterize methylation data around TF binding sites and the background. Along with other static genomic features, we adopted a random forest framework to predict TF-DNA interaction. After conducting comprehensive tests, we saw that the proposed method accurately predicts TF binding and performs favorably versus competing methods. Examine Oct4 genome-wide binding in mouse embryonic stem cells (E14)

2015-03-02 | E-GEOD-65093 | biostudies-arrayexpress

OSKM factors cooperatively engage chromatin to initiate reprogramming

Project description:Reprogramming cells from one fate to another, using transcription factors, generates cells for research and potential therapy, yet little is known about the initial engagement of reprogramming factors with the genome. We mapped the interactions between Oct4, Sox2, Klf4, and c-Myc (OSKM) and the human genome during the first 48 hours of cellular reprogramming to pluripotency. Unlike that reported in ES/iPS cells, we find extensive overlap in the initial binding of OSKM, demonstrating that the initial regulatory network differs markedly from that in pluripotency. OSK act as pioneer factors for c-Myc, and c-Myc enhances the engagement of OSK, including at many genes that are required for conversion to pluripotency. Distal enhancer sites in closed chromatin dominate the initial OSKM distribution. Hierarchical chromatin binding during reprogramming resembles that employed during development. Four chIP-seq data sets (Oct4, Sox2, Klf4, and c-Myc) are included, one lane per factor, no replicates. Also included is an input lane from the same conditions and two mock lentiviral controls (no exogenous OSKM factors) treated with Oct4 IP and c-Myc IP.

2012-11-16 | E-GEOD-36570 | biostudies-arrayexpress

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