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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Genome-wide mapping of Sox6 binding sites in mouse fetal myotubes

ABSTRACT: In order to understand how Sox6 coordinately regulates the transcription of multiple fiber type specific genes during muscle development, we have performed ChIP-seq analyses to identify Sox6 target genes as well as RNA polymerase II (Pol II) binding sites in mouse fetal myotubes. Examination of Sox6 and Pol II binding sites in mouse fetal primary myotubes

ORGANISM(S): Mus musculus

SUBMITTER: Chungil An

PROVIDER: E-GEOD-32627 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genome-wide mapping of Sox6 binding sites in skeletal muscle reveals both direct and indirect regulation of muscle terminal differentiation by Sox6.

An Chung-Il CI Dong Yao Y Hagiwara Nobuko N

BMC developmental biology 20111010

<h4>Background</h4>Sox6 is a multi-faceted transcription factor involved in the terminal differentiation of many different cell types in vertebrates. It has been suggested that in mice as well as in zebrafish Sox6 plays a role in the terminal differentiation of skeletal muscle by suppressing transcription of slow fiber specific genes. In order to understand how Sox6 coordinately regulates the transcription of multiple fiber type specific genes during muscle development, we have performed ChIP-se ...[more]

PMID: 21985497

Similar Datasets

Genome-wide mapping of Sox6 binding sites in mouse fetal myotubes

Project description:In order to understand how Sox6 coordinately regulates the transcription of multiple fiber type specific genes during muscle development, we have performed ChIP-seq analyses to identify Sox6 target genes as well as RNA polymerase II (Pol II) binding sites in mouse fetal myotubes.

2011-10-06 | GSE32627 | GEO

CUT&RUN HUDEP1 OE SOX6-Flag

Project description:SOX6 CUT&RUN on HUDEP1 over expressing SOX6-Flag. The experiment is done using and anti Flag Ab to assist the genome wide binding profile of SOX6 in HUDEP1 (Human Umbilical cord blood-Derived Erythroid Progenitor-1).

2023-04-07 | E-MTAB-12800 | biostudies-arrayexpress

Sox5 and Sox6 direct a cardiac adaptive response to pressure overload

Project description:Rationale: We previously demonstrated that the transcription factor Sox6 regulates skeletal muscle biology by determining myofiber composition and muscle performance. Although the role of Sox6 and Sox5, its closest paralog, has not been ascertained in the heart, genome-wide association studies linked both Sox5 and Sox6 to cardiovascular disease. Objective: This study identifies the role of Sox5 and Sox6 in the adult mammalian heart under normal and stress conditions. Methods and Results: Using Sox5 and Sox6 cardiac-specific and Sox5 conduction system-specific knockout mice, we investigated the role of the two transcription factors in the heart under normal conditions and during cardiac stress. Sox5/6-deficient (DKO) mice displayed blunted cardiac contractility, which was present in Sox5 but not Sox6 single KO mice. DKO mice had a mild reduction in blood pressure, and conduction-specific knockout of Sox5 resulted in a reduced heart rate at baseline. After cardiac pressure overload, DKO mice showed increased lethality compared to control mice and were more prone to develop heart failure. We performed RNA deep sequencing in ventricles from DKO and control mice to identify potential Sox5/6 target genes and found altered expression of genes encoding regulators of calcium handling and cation transporters. Patch-clamping in isolated cardiomyocytes revealed shortened action potential duration in Sox5 KO cells. Conclusions: Unlike in skeletal muscle, our results suggest Sox5 but not Sox6 to be a major regulator of cardiac function and rhythm. Sox5 is essential to preserve cardiac function under normal conditions by maintaining contractility and to prevent cardiac failure after pressure overload.

2018-08-05 | GSE60538 | GEO

Mus musculus

Project description:Genome-wide mapping of Sox6 binding sites in mouse fetal myotubes

| PRJNA147805 | ENA

The transcription factor SOX6 contributes to the developmental origins of obesity by promoting adipogenesis through inhibition of Wnt signaling

Project description:The developmental transcription factor SOX6 was found to regulate serum, as well as liver triglycerides in BL6 mice treated with SOX6 antisense gapmers compared to control gapmers. SOX6 was initially discovered as a gene over-expressed in mesenchymal stem cells derived from small for gestational age newborns. We characterized its metabolic function in BL6 mice using the above antisense knockdown approach. BL6 mice were treated with either SOX6 specific or control gapmer oligonucleotides for 48h. Knockdown efficiency was measured in liver and epididymal white adipose tissues and serum levels of triglycerides and cholesterol quantified.

2015-06-26 | E-GEOD-70300 | biostudies-arrayexpress

Sox6 expression distinguishes dorsally and ventrally biased dopamine neurons in the substantia nigra with distinctive properties and embryonic origins

Project description:To determine the molecular differences between ventral Sox6+ and dorsal Sox6- DA neurons, we performed bulk RNA-sequencing in sorted mCherry+ and GFP+ cells from the SNc of adult Sox6-FSF-Cre, Th-2A-Flpo, RC-Frepe mice. Our analysis revealed large and significant differential gene expression between these two populations.

2021-10-27 | GSE185480 | GEO

Transcriptome dynamics and potential roles of Sox6 in the postnatal heart

Project description:To gain an integrated view of the dynamic changes in gene expression during postnatal heart development at the organ level, time-series transcriptome analyses of the postnatal hearts of neonatal through adult mice (P1, P7, P14, P30, and P60) were performed using a newly developed bioinformatics pipeline. Additionally, the role of the transcription factor Sox6 in the postnatal maturation of cardiac muscle was investigated by differential transcriptome analyses between Sox6 knockout (KO) and control hearts.

2016-11-10 | GSE60958 | GEO

The transcription factor SOX6 contributes to the developmental origins of obesity by promoting adipogenesis through inhibition of Wnt signaling

2015-06-26 | GSE70300 | GEO

SOX6 interacting proteins' identification in K562 cells for the regulation of γ-globin gene expression research

Project description:Human fetal γ-globin gene is developmentally silenced around the birth, and reactivation of γ-globin gene in adulthood sheds new light on ameliorating symptoms of hemoglobin disorders, such as sickle cell disease (SCD) and β-thalassemias. However, the precise regulation process of γ-globin remains incompletely understood. Here, we found that a new protein directly interacted with SOX6 and exerted a significant repression effect on the expression of γ-globin gene in erythroid cells. Further studies have demonstrated that it bound directly to γ-globin gene promoter via octamer binding motif, which in turn suppressed the transcriptional activity of γ-globin gene promoter. Thus, these data indicate that this new protein acts as a novel transcriptional repressor in the regulation of γ-globin gene expression through direct promoter binding, implying a potential alternative therapeutic target for the treatment of SCD and β-thalassemias.

2022-02-16 | PXD024259 | Pride

Chip-seq of H3 in murine embryonic stem cells, myotubes and pro-B cells.

Project description:Nucleosome remodeling results in loss of histone occupancy. To gain insight into variations in H3 occupancy in different murine cell types, chromatin immunoprecipitation coupled with massive parallel sequencing (ChIP-seq) was performed to determine genome wide occupancy of H3 in ES cells, myotubes and pro-B cells. DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. ChIP was performed using an antibody against total H3 in murine ES cells in normal culture conditions, murine ES cells treated with the TGF-beta inhibitor (SB431542, 10uM) for 24 hours, myotubes differentiated for 48 hours and pro-B cells under normal culture conditions.

2010-08-31 | E-GEOD-23830 | biostudies-arrayexpress

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