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Sox9 directs divergent epigenomic states in brain tumor subtypes (RNA-Seq)

ABSTRACT: Sox9 directs divergent epigenomic states in brain tumor subtypes (RNA-Seq)

PROVIDER: PRJNA837891 | ENA |

REPOSITORIES: ENA

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Sox9 directs divergent epigenomic states in brain tumor subtypes

Project description:Epigenetic dysregulation is a universal feature of cancer that results in altered patterns of gene expression that drive malignancy. Brain tumors exhibit subtype-specific epigenetic alterations, however the molecular mechanisms responsible for these diverse epigenetic states remain unclear. Here we show that the developmental transcription factor Sox9 differentially regulates epigenomic states in high-grade glioma (HGG) and ependymoma (EPN). These contrasting roles for Sox9 correspond with protein interactions with histone deacetylating complexes in HGG, and association with the Rela oncofusion in EPN. Together, our studies demonstrate how epigenomic states are differentially regulated in distinct subtypes of brain tumors, while revealing divergent roles for Sox9 in HGG and EPN tumorigenesis.

2022-07-13 | PXD033863 | Pride

Sox9 directs divergent epigenomic states in brain tumor subtypes

Project description:Sox9 directs divergent epigenomic states in brain tumor subtypes

| PRJNA837883 | ENA

Sox9 directs divergent epigenomic states in brain tumor subtypes (ChIP-Seq)

Project description:Sox9 directs divergent epigenomic states in brain tumor subtypes (ChIP-Seq)

| PRJNA837888 | ENA

Sox9 directs divergent epigenomic states in brain tumor subtypes (ChIP-Seq)

Project description:The goal of this study was to profile active H3K27ac marks between autochthonous mouse models of high-grade glioma (HGG) and ependymoma (EPN). Furthermore, with the objective of how transcription factor Sox9 affect H3K27ac states in these two models, we also profiled H3K27ac status between HGG and EPN after Sox9 overexpression (Sox9-GOF) or deletion (Sox9-LOF) in each of these models. In addition, we extended our studies to evaluate both H3K27ac and Sox9 states in human HGG and mouse EPN derived tumor cells.

2022-05-20 | GSE202960 | GEO

Sox9 directs divergent epigenomic states in brain tumor subtypes (RNA-Seq)

Project description:The goal of this study was to profile gene expression differences between autochthonous mouse models of high-grade glioma (HGG) and ependymoma (EPN). Furthermore, with the objective of how transcription factor Sox9 affect gene expression in these two models, we also profiled gene expression differences between HGG and EPN after Sox9 overexpression (Sox9-GOF) or deletion (Sox9-LOF) in each of these models.

2022-05-20 | GSE202958 | GEO

Sox9 directs divergent epigenomic states in brain tumor subtypes

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

2022-05-20 | GSE202961 | GEO

Expression profiling of zebrafish sox9 mutants reveals that Sox9 is required for retinal differentiation

Project description:The transcription factor gene Sox9 plays various roles in development, including differentiation of the skeleton, testes, glia, and heart. Other functions of Sox9 remain enigmatic. Because Sox9 protein regulates expression of target genes, the identification of Sox9 targets should facilitate an understanding of the mechanisms of Sox9 action. To help identify Sox9 targets, we used microarray expression profiling to compare wild-type embryos to mutant embryos lacking activity for sox9a and sox9b, the zebrafish co-orthologs of Sox9. Candidate genes were further evaluated by whole mount in situ hybridization in wild-type and sox9 mutant embryos. Results identified genes expressed in cartilage (col2a1a and col11a2), retina (calb2a, calb2b, crx, neurod, rs1, sox4a and vsx1) and pectoral fin bud (klf2b and EST AI722369) as candidate targets for Sox9. Cartilage is a well-characterized Sox9 target, which validates this strategy, whereas retina represents a novel Sox9 function. Analysis of mutant phenotypes confirmed that Sox9 helps regulate the number of MÃ¼ller glia and photoreceptor cells and helps organize the neural retina. These roles in eye development were previously unrecognized and reinforce the multiple functions that Sox9 plays in vertebrate development. In each experiment, RNA was isolated from 48h wildtype and sox9a, sox9b double mutant embryos and the gene expression profiles were compared using microarrays. Three biological replicate experiments were performed, and each biological replicate contained a dyeswap.

2010-05-16 | E-GEOD-13482 | biostudies-arrayexpress

Profiling of Sox9-related genes in chondrogenesis using Sox9-3'EGFP knock-in and Sox9-EGFP/EGFP null chimeric mouse embryos

Project description:To define the repertoire of Sox9-dependent genes that contribute to the regulation of chondrogenesis, we generated Sox9-3'enhanced green fluorescent protein (EGFP) knock-in mice (Sox9-3'EGFP) and Sox9-EGFP/EGFP null chimeras. EGFP-positive cells of Sox9-3'EGFP knock-in and Sox9-EGFP/EGFP null chimeric embryos harvested from limb buds at embryonic day 12.5 were sorted using a FACSAria flow cytometer (Becton-Dickinson). Total RNA of sorted cells was extracted using the RNeasy Mini Kit (QIAGEN) and amplified according to the instructions provided by Affymetrix. Microarray analysis using the Affymetrix Mouse Genome 430 2.0 Array was performed according to the manufacturer's instructions.

2011-02-16 | E-MTAB-537 | biostudies-arrayexpress

SOX9 overexpression in melanoma

Project description:SOX9 is generally not expressed in melanomas with a high proliferative capacity but is expressed in melanomas with a high invasive capacity. Here we overexpress full length SOX9 in M010817, a melanoma cell culture with high proliferative capacity but low invasive capacity. 3x Control vector. 3x SOX9 overexpression

2014-05-09 | E-GEOD-57463 | biostudies-arrayexpress

Genes regulated by Sox9

Project description:We compared gene expression profile of jejunum crypt samples of Sox9 deficient mice and wild type control mice in order to identify the genes that are regulated by SOX9 in the small intestinal crypt epithelial cells. The intestinal epithelial cells were collected from crypts of jejunum of three 3-mo-old Sox9 mutant mice and three littermate controls.

2012-03-23 | E-GEOD-35481 | biostudies-arrayexpress

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