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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Chip-Seq analysis of Sox2 protein genome-wide DNA binding sites in glioma cancer cells

ABSTRACT: We report here our results of the genome wide target identification of SOX2 in GBM cells by ChIP-seq analysis. Identification of Sox2 DNA binding site in glioma cancer cells

ORGANISM(S): Homo sapiens

SUBMITTER: Biao Yang Lin

PROVIDER: E-GEOD-23795 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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The SOX2 response program in glioblastoma multiforme: an integrated ChIP-seq, expression microarray, and microRNA analysis.

Fang Xuefeng X Yoon Jae-Geun JG Li Lisha L Yu Wei W Shao Jiaofang J Hua Dasong D Zheng Shu S Hood Leroy L Goodlett David R DR Foltz Gregory G Lin Biaoyang B

BMC genomics 20110106

<h4>Background</h4>SOX2 is a key gene implicated in maintaining the stemness of embryonic and adult stem cells. SOX2 appears to re-activate in several human cancers including glioblastoma multiforme (GBM), however, the detailed response program of SOX2 in GBM has not yet been defined.<h4>Results</h4>We show that knockdown of the SOX2 gene in LN229 GBM cells reduces cell proliferation and colony formation. We then comprehensively characterize the SOX2 response program by an integrated analysis us ...[more]

PMID: 21211035

Similar Datasets

An integrative analysis of the SOX2 response program in glioblastoma

Project description:This SuperSeries is composed of the following subset Series: GSE23795: Chip-Seq analysis of Sox2 protein genome-wide DNA binding sites in glioma cancer cells GSE23838: Genes regulated by Sox2 in glioma cancer cell line Refer to individual Series

2011-01-10 | E-GEOD-23839 | biostudies-arrayexpress

Genomic rewiring of Sox2 chromatin interaction network during differentiation of ESCs to postmitotic neurons

Project description:Cellular differentiation requires cells to undergo dramatic but strictly controlled changes in chromatin organization, transcriptional regulation, and protein production and interaction. To understand the regulatory connections between these processes, we applied a multi-omics approach integrating proteomic, transcriptomic, chromatin accessibility, protein occupancy, and protein-chromatin interaction data acquired during differentiation of mouse embryonic stem cells (ESCs) into post-mitotic neurons. We found extensive remodeling of the chromatin that was preceding changes on RNA and protein levels. We found the pluripotency factor Sox2 as regulator of neuron-specific genes and, as a potential mechanism, revealed its genomic redistribution from pluripotency enhancers to neuronal promoters and concomitant change of its protein interaction network upon differentiation. We identified Atrx as a major Sox2 partner in neurons, whose co-localisation correlated with an increase in active enhancer marks and increased expression of nearby genes, and where deletion of a Sox2-Atrx co-bound site resulted in reduced expression of the proximal gene. Collectively, these findings provide key insights into the regulatory transformation of Sox2 during neuronal differentiation and highlight the significance of multi-omic approaches in understanding gene regulation in complex systems.

2020-06-04 | PXD016080 | Pride

Development of a method for quantitative analysis of in vivo interactions of pluripotency transcription factors Sox2, Oct4, Nanog by mass spectrometry

Project description:Protein-protein proximity of core pluripotency transcription factors plays an important role during cell reprogramming. Pluripotent embryonic stem (ES) cell identity is controlled by a trio of transcription factors: Sox2, Oct4, and Nanog. These proteins often bind to closely localized genomic sites. The precise mode by which Sox2, Oct4, and Nanog interact with DNA is likely to make a crucial contribution to their function. Here, a detailed protocol for in vivo detection and quantitative analysis of protein-protein proximity of Sox2 and Oct4 using Proximity Utilizing Biotinylation (PUB) method based on the use of the BAP/BirA (target/enzyme) system is described. The method includes design and cloning of DNA plasmid construct, transient transfection of HEK293T cells, Western blot analysis of nuclei fraction and LC-MS/MS analysis. Experiments with coexpression of BAP-X+BirA-Y (X, Y=Sox2, Oct4 and GFP as control) revealed strong biotinylation level of target proteins when X and Y were pluripotency transcription factors compared with control when X=GFP. Since mass spectrometry provides both high sensitivity and more accurate quantification of data a modified workflow was used, in which SDS-PAGE step was eliminated and His-tagged BAP-fused proteins from cell lysate were purified in 6M guanidine HCl buffer, washed, propionylated, digested directly on the Ni sepharose beads using trypsin and analysed on Q-TOF Impact II instrument. Using mass spectrometry allows making quantitative estimation of in vivo interaction of BAP-Sox2 and BirA-Oct4 which was demonstrated by measuring ratios of biotinylation levels of BAP fused either with Sox2 or GFP at different biotin pulse times. After vector preparation this protocol can be completed in seven working days.

2020-01-21 | PXD015756 | Pride

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

ChIP-chip of MCF7 Sox2 regulatory region 2 transcription activity reporter unresponsive and reporter responsive breast cancer cells

Project description:We found that MCF7 and ZR751 Sox2-expressing breast cancer cell lines comprise of cells with heterogeneous Sox2 transcription activity reporter response. A small subset of Sox2 reporter responsive cells are more tumourigenic than the bulk Sox2 reporter unresponsive cells. We questioned whether Sox2 exhibit differential gene promoter occupancies in the two cell subsets to govern differential gene expression patterns. Sox2 ChIP in reporter unresponsive (RU) and reporter responsive (RR) cells (duplicate samples) were compared. IgG ChIP in RU and RR cells served as the negative controls.

2014-09-25 | E-GEOD-61703 | biostudies-arrayexpress

Competitive binding of E3 ligases TRIM26 and WWP2 controls SOX2 in glioblastoma

Project description:The pluripotency transcription factor SOX2 is essential for the maintenance of glioblastoma stem cells (GSC), which drive tumor growth and treatment resistance.To understand how SOX2 is regulated in GSCs, we utilized a proteomic approach and identified the E3 ubiquitin ligase TRIM26 as a direct SOX2-interacting protein. Unexpectedly, we found TRIM26 depletion decreased SOX2 protein levels and increased SOX2 polyubiquitination in patient-derived GSCs, suggesting TRIM26 promotes SOX2 protein stability. Accordingly, TRIM26 knockdown reduced SOX2 transcriptional activity, self-renewal capacity, and in vivo tumorigenicity in multiple GSC lines. Mechanistically, we found TRIM26, via its C-terminal PRYSPRY domain, but independent of its RING domain, stabilizes SOX2 protein by directly inhibiting the interaction of SOX2 with WWP2, which we identify as a bona fide SOX2 E3 ligase in GSCs. Our work identifies E3 ligase competition as a critical mechanism of SOX2 regulation, with functional consequences for GSC identity and maintenance.

2021-11-04 | PXD028933 | Pride

Sox2 suppresses gastric tumorigenesis in mice [CHIP-seq]

Project description:Purpose: Sox2 expression marks gastric stem and progenitor cells, raising important questions regarding the genes regulated by Sox2 and the role of Sox2 itself during stomach homeostasis and disease. The goal of this study is to determine the function of and the genes regulated by Sox2 in the stomach. Methods: Sox2 ChIP-enriched DNA and input DNA was isolated from gastric glands of adult antrum from Sox2 KO and Sox2 WT mice. DNA was purified and genomic libraries were prepared as described (Sulahian et al., 2014), using four micrograms of goat anti-SOX2 (AF2018, R&D). Libraries were sequenced (50 bp, single-end reads) on an Illumina Hi-Seq 2000 instrument. Results: Sox2 is dispensiable for gastric stem cell self-renewal and epithelial homeostasis, however modulates the expression of wnt, intestinal and cancer related genes Examination of Sox2 targets in the stomachs of Sox2 WT and Sox2 KO mice.

2016-08-04 | E-GEOD-83965 | biostudies-arrayexpress

SOX4 genome binding targets in glioblastoma cell line

Project description:Overexpression of SOX4 in LN229 glioblastoma cells prevents their cell cycle Examination of SOX4 binding profile in prostate cell LN229-SOX4 with LN229-GFP as negative control.

2014-10-20 | E-GEOD-51663 | biostudies-arrayexpress

RIP-seq to identify transcripts interacting with pluripotency factors in mouse embryonic stem cells

Project description:Sox2 is a master transcriptional regulator of embryonic development. Having found that Sox2 interacts with RNA-binding proteins, we designed an experiment to discover RNAs associated with Sox2 and other pluripotency factors. Briefly, we used RNA immunoprecipitation followed by high-throughput sequencing (RIP-seq) to sequence transcriptomes enriched for RNAs associated with Klf4, Nanog, Oct4, Sox2 and Suz12. For completeness, this submission includes all RIP-seq data from this study, although some of the data was only used for exploratory analyses. Such analysis indicated that it was important to include input samples for each of the the cell lines that were to be compared, to account for differences in gene expression (e.g. between J1-birA with and without bioSox2), and that overnight IP was more informative than 3 h IP. Therefore, the analysis described in the associated manuscript used samples from experiment batch 3 and 4 only (samples 11-18).

2019-02-11 | E-MTAB-7640 | biostudies-arrayexpress

ChIP-seq after immunoprecipitation with either IgG or SOX2 antibodies in murine genetically modified stem cells overexpressing the RAX gene (CCE-Rx cells)

Project description:In order to identify target genes of the SOX2 transcription factor, we tried to identify SOX2 binding site in murine genetically modified stem cells overexpressing the RAX gene (CCE-Rx cells) by ChIP-seq. SOX2 gene mutations are involved in anophthalmia and our hypothesis was that target genes of SOX2 transcription factor may also be candidate to be involved in ocular development. High throughput sequencing after chromatin immunoprecipitation using either an antibody against our target transcription factor (SOX2) or using control antobodies (IgG). These experiments were performed on only one immunoprecipitation with each antibody.

2015-11-04 | E-GEOD-74599 | biostudies-arrayexpress

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