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Sox7 and Sox17

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

ORGANISM(S): Mus musculus

SUBMITTER: Irene Aksoy

PROVIDER: E-GEOD-43234 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Oct4 switches partnering from Sox2 to Sox17 to reinterpret the enhancer code and specify endoderm.

Aksoy Irene I Jauch Ralf R Chen Jiaxuan J Dyla Mateusz M Divakar Ushashree U Bogu Gireesh K GK Teo Roy R Leng Ng Calista Keow CK Herath Wishva W Lili Sun S Hutchins Andrew P AP Robson Paul P Kolatkar Prasanna R PR Stanton Lawrence W LW

The EMBO journal 20130308 7

How regulatory information is encoded in the genome is poorly understood and poses a challenge when studying biological processes. We demonstrate here that genomic redistribution of Oct4 by alternative partnering with Sox2 and Sox17 is a fundamental regulatory event of endodermal specification. We show that Sox17 partners with Oct4 and binds to a unique 'compressed' Sox/Oct motif that earmarks endodermal genes. This is in contrast to the pluripotent state where Oct4 selectively partners with Sox ...[more]

PMID: 23474895

Similar Datasets

Gene expression analysis of F9 cells double knock-down for Sox7 and Sox17

Project description:Analysis of the expression of F9 cells after knockdown of Sox7 and Sox17 during their primitive endoderm differnetiation induction with retinoic acid. Results provide information on the endodermal gene expression program regulated by Sox7 and Sox17. Sox7 Sox17 double KD vs. control in F9 cells

2013-04-23 | E-GEOD-43232 | biostudies-arrayexpress

Gene expression analysis of V5 tagged Sox17 expressing ES cells

Project description:Analysis of the expression of KH2 embryonic stem cells inducibly expressing V5 tagged Sox17 protein. Results provide information on the endodermal gene expression program activated after Sox17 expression in ES cells. Total RNA extracted from 48 hours doxycycline induced compaired to non-induced Sox17-V5 expressing ES cells

2013-04-23 | E-GEOD-43233 | biostudies-arrayexpress

Sox7 and Sox17

Project description:This SuperSeries is composed of the SubSeries listed below.

2013-04-23 | GSE43234 | GEO

Genome wide expression analysis of Ctbp2 knock down mouse F9 cells

Project description:Using an RNA interference-based genetic screen in mouse F9 cells we identify the transcriptional corepressor CTBP2 as a coactivator critically required for retinoic acid (RA)-induced transcription. Here we perfom a whole genome transcriptome analysis in F9 cells expressing shRNA for Ctbp2 and Rxr in the absence or presence of retinoic acid (RA). A total of 2,754 genes were found to be upregulated (>2 fold) and 1518 genes were downregulated (>2 fold) in response to RA treatment in the control cells. We find that around 52% and 55% of upregulated genes are dependent on Ctbp2 and Rxr for activation respectively suggesting that Ctbp2 is a coactivator of RA signaling. Whole genome RNA-sequencing in F9 cells expressing shGFP or shCtbp2 or shRxr

2013-06-21 | E-GEOD-47708 | biostudies-arrayexpress

Sox7, Sox17, and Sox18 Cooperatively Regulate Vascular Development in the Mouse Retina.

Project description:Vascular development and maintenance are controlled by a complex transcriptional program, which integrates both extracellular and intracellular signals in endothelial cells. Here we study the roles of three closely related SoxF family transcription factors-Sox7, Sox17, and Sox18 -in the developing and mature mouse vasculature using targeted gene deletion on a mixed C57/129/CD1 genetic background. In the retinal vasculature, each SoxF gene exhibits a distinctive pattern of expression in different classes of blood vessels. On a mixed genetic background, vascular endothelial-specific deletion of individual SoxF genes has little or no effect on vascular architecture or differentiation, a result that can be explained by overlapping function and by reciprocal regulation of gene expression between Sox7 and Sox17. By contrast, combined deletion of Sox7, Sox17, and Sox18 at the onset of retinal angiogenesis leads to a dense capillary plexus with a nearly complete loss of radial arteries and veins, whereas the presence of a single Sox17 allele largely restores arterial identity, as determined by vascular smooth muscle cell coverage. In the developing retina, expression of all three SoxF genes is reduced in the absence of Norrin/Frizzled4-mediated canonical Wnt signaling, but SoxF gene expression is unaffected by reduced VEGF signaling in response to deletion of Neuropilin1 (Npn1). In adulthood, Sox7, Sox17, and Sox18 act in a largely redundant manner to maintain blood vessel function, as adult onset vascular endothelial-specific deletion of all three SoxF genes leads to massive edema despite nearly normal vascular architecture. These data reveal critical and partially redundant roles for Sox7, Sox17 and Sox18 in vascular growth, differentiation, and maintenance.

| S-EPMC4667919 | biostudies-literature

Dissecting the retinoid-induced differentiation of F9 embryonal stem cells by integrative genomics [ChIP-seq]

Project description:Retinoic acid (RA) triggers physiological processes by activating heterodimeric transcription factors comprising retinoic acid (RARa,b,g) and retinoid X (RXRa,b,g) receptors. How a single signal induces highly complex temporally controlled networks that ultimately orchestrate physiological processes is unclear. Using an RA-inducible differentiation model we defined the temporal changes in the genome-wide binding patterns of RARg and RXRa and correlated them with transcription regulation. Unexpectedly, both receptors displayed a highly dynamic binding, with different RXRa heterodimers targeting identical loci. Comparison of RARg and RXRa co-binding at RA-regulated genes identified putative RXRa-RARg target genes that were validated with subtype-selective agonists. Gene regulatory decisions during differentiation were inferred from transcription factor target gene information and temporal gene expression. This analysis revealed 6 distinct co-expression paths of which RXRa-RARg is associated with transcription activation, while Sox2 and Egr1 were predicted to regulate repression. Finally, RXRa-RARg regulatory networks were reconstructed through integration of functional co-citations. Our analysis provides a dynamic view of RA signalling during cell differentiation, reveals RA heterodimer dynamics and promiscuity, and predicts decisions that diversify the RA signal into distinct gene-regulatory programs. RXRa; RARg and RNA Polymerase II chromatin binding has been assessed at five time points; in addition an input control for F9 cells as well as a RXRa ChIP-seq assay from a rxra-/- ko strain has been performed.

2011-10-11 | E-GEOD-30538 | biostudies-arrayexpress

Dissecting the retinoid-induced differentiation of F9 embryonal stem cells by integrative genomics

Project description:This SuperSeries is composed of the following subset Series: GSE30537: Dissecting the retinoid-induced differentiation of F9 embryonal stem cells by integrative genomics [mRNA profiling] GSE30538: Dissecting the retinoid-induced differentiation of F9 embryonal stem cells by integrative genomics [ChIP-seq] Refer to individual Series

2011-10-10 | E-GEOD-30539 | biostudies-arrayexpress

Transcript level in F9 teratocarcinoma WT and RARalpha knockout in presence and absence of all-trans retinoic acid

Project description:Retinoic acid receptors (RARs) α, β and γ are key regulators of embryonic development. Hematopoietic differentiation is regulated by RARα, and several types of leukemia show aberrant RARα activity. We demonstrate that RARα plays an important role in cellular memory and imprinting by regulating the CpG methylation status of specific promoter regions. We used microarrays to identify genes, which display differential expression in F9 RARalpha knockout (RARaKO) cells relative to F9 wt cells. F9 teratocarcinoma cells (WT and RARaKO) were treated for 8 hours with either vehicle (EtOH) or all-trans Retinoic Acid (atRA) in the presence of the protein synthesis inhibitor Cycloheximide

2011-08-09 | E-GEOD-31280 | biostudies-arrayexpress

HUVEC gene profile after Sox7/Sox17 siRNA silencing

Project description:To find out the target of transcription factor Sox7 and Sox17, DNA microarray analysis was performed with RNA from Sox7 and Sox17 knockdown HUVECs.

2016-11-23 | GSE75380 | GEO

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

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