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Expression data from MCF-7 Human Breast Cancer Cells

ABSTRACT: SOX genes encode a family of high-mobility group transcription factors that play critical roles in organogenesis. Virtually all members of SOX family have been found to be deregulated in tumors of various origins. However, little is known about the cellular and molecular behaviours involved in the oncogenic potential of SOX proteins. Cell culture experiments, tissue analysis, and molecular profiling revealed that SOX2 promotes cell proliferation and tumorigenesis through its transcription regulation of cell cycle related genes in breast cancer cells Keywords: Gene Transfection

ORGANISM(S): Homo sapiens

PROVIDER: GSE11330 | GEO | 2009/05/02

SECONDARY ACCESSION(S): PRJNA106655

REPOSITORIES: GEO

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Transcription profiling of MCF-7 Human Breast Cancer Cells

Project description:SOX genes encode a family of high-mobility group transcription factors that play critical roles in organogenesis. Virtually all members of SOX family have been found to be deregulated in tumors of various origins. However, little is known about the cellular and molecular behaviours involved in the oncogenic potential of SOX proteins. Cell culture experiments, tissue analysis, and molecular profiling revealed that SOX2 promotes cell proliferation and tumorigenesis through its transcription regulation of cell cycle related genes in breast cancer cells Experiment Overall Design: To delineate the molecular mechanism underlying the cell proliferation and tumorigenic properties of SOX2, we investigated the gene expression profile in MCF-7 cells. Briefly, MCF-7 cells were transfected with pcDNA3.1 and Human SOX2 expression constructs respectively. 24 hours after transfection, total RNA collected from control and SOX2-overexpressing MCF-7 cells was used to probe Human Genome GeneChip array U133 Plus 2.0

2009-05-11 | E-GEOD-11330 | biostudies-arrayexpress

HUES cells: control and overexpressing OCT4

Project description:HUES24 cell line was nucleofected with POU5f1 cDNA to overexpress OCT4; This leads to the formation of mesendodermal cells Short- and Long-scales intra- and inter-chromosomal interactions are linked to gene transcription, but the molecular event underlying these structures and how it affects cell fate decision during embryonic development are poorly understood. One of the first embryonic cell fate decisions (i.e mesendoderm determination) is driven by the POU factor OCT4, acting in concert with the high mobility group genes SOX-2 and SOX-17. Here, we identify novel chromatin remodelling mechanism and enhancer function driven by both OCT4 and SALL4 that mediate cell fate switching. We found that OCT4 alters the higher-order chromatin structure at both Sox-2 and Sox-17 loci. OCT4 titrates out cohesin and switches the Sox-17 enhancer from a locked (within an inter-chromosomal Sox-2 enhancer/CTCF/cohesin loop) to an active (within an intra-chromosomal Sox-17 promoter/enhancer/cohesin loop) state. SALL4 concomitantly mobilizes the polycomb complexes at the Soxs loci. Thus, OCT4/SALL4-driven cohesin-and polycombs-mediated changes in higher order chromatin structure mediate instruction of early cell fate in embryonic cells. ChIP anti-OCT4 on chip. results_v2.xls file description: Enriched binding sites. Mutant means oct4 overexpressing cells , wt GFP nucleofected cells.

2015-04-02 | E-GEOD-58125 | biostudies-arrayexpress

HUES cells: control and overexpressing OCT4

2015-04-02 | GSE58125 | GEO

Molecular characterization and differential expression profiles of transcription factor Sox gene family between ovaries and testes from golden pompano （Trachinotus ovatus）

Project description:The SRY-related HMG-box (Sox) is a transcription factor related to the testis-determining gene SRY (Sex determination Region of Y chromosome), which plays an important role in the sexual development of Osteichthyes. In order to understand the characteristics of Sox gene family members in Trachinotus ovatus（ToSox）, this study used bioinformatics methods to systematically analyze the physicochemical properties, phylogenetic tree, chromosomal localization, and prediction of interacting proteins of the ToSsxs. The expressions of the ToSoxs were analyzed using transcriptomics data from ovary and testis of T. ovatus. The results showed that 18 members of Sox gene family were identified, and the members of the family were hydrophilic proteins with large differences in amino acid number, molecular weight and isoelectric point. The evolutionary tree analysis showed that the Sox family genes were divided into seven branches (B1, B2, C, D, E, F, H) The chromosomal localization analysis showed that these genes of the family were scattered on 15 chromosomes. The structure of Sox genes was simple and relatively conserved. Intraspecific covariance analysis revealed that one pair of ToSox gene covariance, and interspecific covariance analysis revealed 14 pairs of collinearities between T. ovatus and zebrafish and 20 pairs of collinearities between T. ovatus and tilapia. The members of ToSox proteins had close interactions with one another, and with other proteins as well. The results of transcriptome analysis showed that the genes ToSox30, ToSox1a, ToSox17, ToSox11, ToSox9b, and ToSox9b are likely to regulate the testicular development of oviparous jacks, which is related to male sex determination. This study preliminarily investigated the characterization of Sox genes in the T. ovatus genome and provided theoretical references for the study of the effects of Sox transcription factors on sex determination in T. ovatus.

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The emergence of the stem cell-associated Sox and POU transcription factors predates animal origins (SELEX)

Project description:Pluripotent stem cells are a hallmark of animal multicellularity. Sox and POU family transcription factors are pivotal for stemness and were believed to be animal innovations as they were reported absent from the genomes of their unicellular relatives. Here we describe new unicellular holozoan orthologues to Sox and POU families, indicating that they emerged before the appearance of animals. We show that choanoflagellate and filasterean Sox genes have DNA binding specificity similar to Sox2. Choanoflagellate Sox can partner with the POU member Oct4 on DNA elements found in pluripotency enhancers. Consistently, choanoflagellate – but not filasterean – Sox genes can replace Sox2 to reprogram mouse somatic cells into induced pluripotent stem cells (iPSC). In contrast, choanoflagellate POU harbors a unique DNA-binding profile that differs from Oct4 and cannot generate iPSCs. Pluripotency reprogramming with reconstructed ancestral Sox genes shows that their molecular ability to induce stemness was already present in the last common ancestor of animals and their unicellular relatives. Our findings imply that the evolution of stem cells exploited a pre-existing set of transcription factors, where the critical innovation involved an initial change in DNA specificity of POU and the exaptation of the ancestral capacity to interact with Sox transcription factors.

2024-10-23 | GSE253887 | GEO

The emergence of the stem cell-associated Sox and POU transcription factors predates animal origins (Spec-Seq)

2024-10-23 | GSE253886 | GEO

Complex transcription factor networks and sex hormones synergically regulate sexually dimorphic gene expression in PiC neurons

Project description:Investigate cellular and molecular control of sexually dimorphic behaviours in PiC neurons

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Three-dimensional molecular architecture of mouse organogenesis

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Expression data from Rb family deficient Cd150+ HSC

Project description:Loss of Rb family in HSC results in their sustained proliferation, impaired homeostasis and extramedullar mobility.

2017-05-24 | GSE98311 | GEO

High-resolution genome replication profiles, modeling and single-cell imaging define the stochastic nature of replication initiation and termination

Project description:Eukaryotic genome replication is stochastic with each cell using a different cohort of replication origins. Interpreting high-resolution genome replication profiles with a mathematical model allowed us to quantify the stochastic nature of genome replication. This approach included estimation of the activity of every replication origin and the genome-wide location of replication termination events. Single-cell measurements verified the inferred values for stochastic origin replication time. Strains in which multiple origins had been inactivated, confirmed that the location of termination events is primarily dictated by the stochastic activation time of origins. Cell-to-cell variability in origin activity ensures that termination events are widely distributed across virtually the whole genome. We propose that the heterogeneity in origin usage contributes to genome stability by limiting potentially deleterious events from accumulating at particular loci. Measurement of genome replication time for two S. cerevisiae strains. For each strain six S phase samples werecompared with a non-replicating sample.

2013-11-07 | E-GEOD-48561 | biostudies-arrayexpress

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