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ChIP-seq analysis of Esrrb, Nanog, Oct4, and Sox2 in EpiSCs undergoing reprogramming

ABSTRACT: To investigate the molecular mechanisms underlying the reprogramming of epiblast stem cells (EpiSCs) into embryonic stem cells (ESCs) induced by Esrrb, we performed ChIP-seq analysis of Esrrb, Nanog, Oct4, and Sox2 in Tet-on Esrrb EpiSCs after treatment with doxycycline (Dox).

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Mus musculus

SUBMITTER: Bernd Timmermann

PROVIDER: E-MTAB-5342 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Microarray analysis of EpiSCs undergoing reprogramming by Esrrb.

Project description:To characterize the reprogramming of epiblast stem cells (EpiSCs) into embryonic stem cells (ESCs) induced by Esrrb, we performed microarray analysis of Tet-on Esrrb EpiSCs after treatment with doxycycline (Dox).

2018-06-01 | E-MTAB-5341 | biostudies-arrayexpress

BMP signaling in mouse embryonic stem cells (ESCs) in the naÃ¯ve and primed pluripotent states [ChIP-Seq]

Project description:Carrying out both RNA-seq and Smad1/5 genome-wide chromatin immunoprecipitation and sequencing (ChIP-seq) analyses of mESCs in the naÃ¯ve or primed states, we revisit the roles of BMP signaling in mESCs. Smad1/5 binding sites in 2 cell types; mESCs and ES-derived EpiSC (ESD-EpiSCs).

2015-12-04 | E-GEOD-70579 | biostudies-arrayexpress

Messenger RNA profile analysis deciphers new Esrrb responsive genes in prostate cancer cells

Project description:We report nuclear receptor Esrrb's responsive genes with or without Esrrb ligand DY131 in DU145 cells. Using Esrrb-null cells, we used RNA-Seq to find Esrrb responsive genes. In addition, we tested DY131-driven Esrrb-dependent genes to test the ligand dependency of Esrrb in regulating gene expression. Control vector transfected cells with vehicle treatment, Esrrb expression vector transfected cell with vehicle treatment, control vector transfected cells with DY131 treatment, Esrrb expression vector transfected cell with DY131 treatment.

2015-11-06 | E-GEOD-71208 | biostudies-arrayexpress

BMP signaling in mouse embryonic stem cells (ESCs) in the naÃ¯ve and primed pluripotent states

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-12-04 | E-GEOD-70581 | biostudies-arrayexpress

Fgf and Esrrb integrate epigenetic and transcriptional networks that regulate self-renewal of Trophoblast Stem Cells

Project description:Esrrb is a transcription factor implicated in embryonic stem (ES) cell self-renewal, yet its knockout causes intrauterine lethality due to defects in trophoblast development. Here we show that in trophoblast stem (TS) cells, Esrrb is a downstream target of fibroblast growth factor (Fgf) signalling and is critical to drive TS cell self-renewal. In contrast to its occupancy of pluripotency-associated loci in ES cells, Esrrb sustains the stemness of TS cells by direct binding and regulation of TS cell-specific transcription factors including Elf5 and Eomes. To elucidate the mechanisms whereby Esrrb controls the expression of its targets, we characterized its TS cell-specific interactome by mass spectrometry. Unlike in ES cells, Esrrb interacts in TS cells with the histone demethylase Lsd1 and with the RNA Polymerase II-associated Integrator complex. Our findings provide new insights into both, the general and context-dependent wiring of transcription factor networks in stem cells by master transcription factors.

2015-07-24 | PXD002183 | Pride

Global gene expression analysis of Ncoa3 knockdown in mouse embryonic stem cells

Project description:Orphan nuclear receptor Esrrb is vital in maintaining ES cells and like Oct4, Sox2 and Nanog is essential for self-renewal and pluripotency. Esrrb functions in somatic cells via LBD/AF-2-dependent coactivator recruitment to target genes. Here we show that in ES cells coactivator recruitment is similarly required and identify Ncoa3 as the Esrrb coactivator needed for activation of its target genes. Ncoa3 is essential for self-renewal and the induction of pluripotency in reprogramming, and genome-wide analysis of Ncoa3 binding reveals extensive overlap with Esrrb and pluripotency factors along with marks of active genes. Mechanistically, we show Ncoa3 is specifically required to bridge RNApol2 to Esrrb. We thus identify a new member of the ES pluripotency network and describe Esrrb and Ncoa3 as key factors linking core pluripotency factors to the general transcription machinery. Three biological replicates each for control scrambled shRNA and Ncoa3 shRNA transfected E14 mouse ESCs. The global gene expression profiles of Ncoa3 knockdown cells were compared to control scrambled shRNA knockdown cells 4 days post-transfection.

2012-10-02 | E-GEOD-40192 | biostudies-arrayexpress

The interactome of POU5F1 upstream enhancer in mouse embryonic stem cells revealed by 4C-Seq

Project description:We report the application of 4C-Seq technique for exploring POU5F1 enhancer interactome in mouse embryonic stem cells. A statistical model was built to identify enriched interacting regions from raw 4C data. The biological replicate data were compared to identify reproducible interacting regions. The interacting sites in the reproducible regions are enriched with active histone marks as well as transcription factors Oct4, Klf4, Esrrb, Tcfcp2i1 and Zfx that are critical for reprogramming and pluripotency. Generation of Illumina HiSeq2000 sequencing data using 4C-Seq protocol

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Next generation unnatural monosaccharides reveal that ESRRBO GlcNAcylation enhances pluripotency of mouse embryonic stem cells

Project description:Unnatural monosaccharides such as azidosugars that can be metabolically incorporated into cellular glycans are currently used as a major tool for glycan imaging and glycoproteomic profiling. As a common practice to enhance membrane permeability and cellular uptake, the unnatural sugars are per O acetylated, which, however, can induce a long-overlooked side reaction, non enzymatic S-glycosylation. Herein, we develop1,3 di esterified N azidoacetylgalactosamine (GalNAz) as the next generation chemical reporters for metabolic glycan labeling. Both 1,3 di O-acetylated GalNAz (1,3-Ac2GalNAz) and1,3 di O propionylated GalNAz (1,3-Pr2GalNAz)exhibited high efficiency for labeling protein O-GlcNAcylation with no artificial S-glycosylation. Applying1,3 Pr2GalNAz in mouse embryonic stem cells (mESCs), we identified ESRRB, a critical transcription factor for pluripotency, as an O-GlcNAcylated protein. We showed that ESRRB O-GlcNAcylation is important for mESC self-renewal and pluripotency. Mechanistically, ESRRB is O-GlcNAcylated by O-GlcNAc transferase (OGT) at serine 25 (Ser 25), which stabilizes ESRRB, promotes its transcription activity and facilitates its interactions with two master pluripotency regulators, OCT4 and NANOG.

2019-09-09 | PXD015035 | Pride

Next generation unnatural monosaccharides reveal that ESRRBO GlcNAcylation enhances pluripotency of mouse embryonic stem cells

2019-09-12 | PXD014785 | Pride

Global gene-expression analyses of the Esrrb knockdown cells

Project description:In the murine system, Oct4, Sox2, c-Myc and Klf4 are sufficient to convert fibroblasts to induced pluripotent stem (iPS) cells that exhibit many characteristics of embryonic stem (ES) cells. Herein, we show that the orphan nuclear receptor Esrrb works in conjunction with Oct4 and Sox2 to mediate reprogramming of mouse embryonic fibroblasts (MEFs) to iPS cells. Esrrb reprogrammed cells share similar expression and epigenetic signatures as ES cells. These cells are also pluripotent and can differentiate in vitro and in vivo into the three major embryonic cell lineages. Furthermore, these cells contribute to mouse chimeras and are germline transmissible. In ES cells, Esrrb targets many genes involved in selfrenewal and pluripotency. This suggests that Esrrb may mediate reprogramming through the up-regulation of ES cell-specific genes. Our findings also indicate that it is possible to reprogram MEFs without exogenous Klf transcription factors and link a nuclear receptor to somatic cell reprogramming. Global gene expression effects of silencing the Esrrb gene. We used microarrays to detail the global programme of gene expression after silencing the Esrrb gene. Keywords: time-course Three biological replicates each for control GFP and Esrrb RNAi. The global gene expression profiles of the Esrrb knockdown cells were compared to control GFP knockdown cells for days 2, 4 and 6.

2010-06-24 | E-GEOD-13212 | biostudies-arrayexpress

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