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Investigation of the physiological functions of PRDM6

ABSTRACT: PRDM6 belongs to the PRDM family of transcriptional repressors that all contain a PR domain and Zinc finger domains. Prdm6 has transcriptional repressor activity. Prdm6 may regulate factors that are involved in the differentiation / proliferation of smooth muscle cells, promoting proliferation. PRDM6 knockouts are embryonic lethal around 12.0 dpc knockout embryos eventually develop edema: cardiovascular defect vascularization defect in the yolk sac: dysorganized angiogenesis Keywords: cDNA array, yolk sac, murine embryo E10.5

ORGANISM(S): Mus musculus

PROVIDER: GSE9065 | GEO | 2008/04/01

SECONDARY ACCESSION(S): PRJNA102577

REPOSITORIES: GEO

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Investigation of the physiological functions of PRDM6

Project description:PRDM6 belongs to the PRDM family of transcriptional repressors that all contain a PR domain and Zinc finger domains. Prdm6 has transcriptional repressor activity. Prdm6 may regulate factors that are involved in the differentiation / proliferation of smooth muscle cells, promoting proliferation. PRDM6 knockouts are embryonic lethal around 12.0 dpc knockout embryos eventually develop edema: cardiovascular defect vascularization defect in the yolk sac: dysorganized angiogenesis 6 homozygote samples (yolk sacs), age 10.5 days, hybridized against a pool of of 6 wildtype samples in 12 replicates including 6 dye swap experiments.

2010-05-22 | E-GEOD-9065 | biostudies-arrayexpress

PRDM6 promotes medulloblastoma by repressing chromatin accessibility and altering gene expression [CUT&Run]

Project description:SNCAIP duplication may promote Group 4 medulloblastoma via induction of PRDM6, a poorly characterized member of the PRDF1 and RIZ1 homology domain-containing (PRDM) family of transcription factors. Here, we investigated the function of PRDM6 in human hindbrain neuroepithelial stem cells and tested PRDM6 as a driver of Group 4 medulloblastoma. We report that human PRDM6 localizes predominantly to the nucleus, where it causes widespread repression of chromatin accessibility and complex alterations of gene expression patterns. Genome-wide mapping of PRDM6 binding reveals that PRDM6 binds to chromatin regions marked by histone H3 lysine 27 trimethylation that are located within, or proximal to, genes. Moreover, we show that PRDM6 expression in neuroepithelial stem cells promotes medulloblastoma. Surprisingly, medulloblastomas derived from PRDM6-expressing neuroepithelial stem cells match human Group 3, but not Group 4, medulloblastoma. We conclude that PRDM6 expression has oncogenic potential but is insufficient to drive Group 4 medulloblastoma from neuroepithelial stem cells. We propose that both PRDM6 and additional factors, such as specific cell-of-origin features, are required for Group 4 medulloblastoma. Given the lack of PRDM6 expression in normal tissues and its oncogenic potential shown here, we suggest that PRDM6 inhibition may have therapeutic value in PRDM6-expressing medulloblastomas.

2024-07-17 | GSE243557 | GEO

PRDM6 promotes medulloblastoma by repressing chromatin accessibility and altering gene expression [ATAC-Seq]

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PRDM6 promotes medulloblastoma by repressing chromatin accessibility and altering gene expression [RNA-Seq]

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Comparison of gene expression pattern between Wild-type and Hypb knockout embryo yolk sacs

Project description:This study aimed at exploring the physiological function of mammalian HYPB by means of knockout mouse model. Homogenous disruption of mouse Hypb gene leads to embryonic lethality at E10.5-E11.5. Severe vascular defects were observed in the Hypb-/- embryos, yolk sac and placenta.In the mutant embryo and yolk sac, disorganized and abnormally dilated capillaries cannot be remodeled into large blood vessels or intricate networks. Thus, our results suggest that the mammalian HYPB HMT plays an important role in embryonic vascularization. Keywords: knockout, mouse embryo development, angiogenesis, yolk sac, E9.0, E10.5

2009-12-28 | GSE10113 | GEO

Gene expression profiling of rudhira null embryo and yolk sac at 9.5 dpc

Project description:Rudhira is essential for mouse developmental angiogenesis and tissue morphogenesis. Embryos lacking endothelial rudhira die at mid-gestation with vascular patterning defects. Rudhira mutant yolk sac endothelial cells show slow and random migration. So to identify key signaling pathways perturbed in the absence of rudhira, we undertook whole transcriptome based analysis of gene expression in rudhira null yolk sac and embryo. Transcriptome analysis shows that key mediators of angiogenesis, cell adhesion, migration and extracellular matrix degradation as well as several components of the TGFÎ² pathway are perturbed in rudhira null mutant yolk sacs at 9.5 dpc. We used two embryo samples ( 2E- wild type; 5E- rudhira mutant). Repetition was done on each sample. We used 4 yolk sac samples (3Y,4Y- wild type; 7Y,8Y-rudhira mutant) for the analysis. Repetition was done on each sample.

2015-12-31 | E-GEOD-69204 | biostudies-arrayexpress

Gene expression profiling of rudhira null embryo and yolk sac at 9.5 dpc

Project description:Rudhira is essential for mouse developmental angiogenesis and tissue morphogenesis. Embryos lacking endothelial rudhira die at mid-gestation with vascular patterning defects. Rudhira mutant yolk sac endothelial cells show slow and random migration. So to identify key signaling pathways perturbed in the absence of rudhira, we undertook whole transcriptome based analysis of gene expression in rudhira null yolk sac and embryo. Transcriptome analysis shows that key mediators of angiogenesis, cell adhesion, migration and extracellular matrix degradation as well as several components of the TGFβ pathway are perturbed in rudhira null mutant yolk sacs at 9.5 dpc.

2015-12-31 | GSE69204 | GEO

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Effect of smooth muscle specific PRDM6 depletion on Aorta and Ductus Arterious (DA) development

Project description:To investigate the function of PRDM6 in smooth muscle cells during outflow tract development, we have isolated the ascending aorta and the ductus arteriosus (DA) separatly from the E18.5 Wnt1Cre;PRDM6f/f mouse (PRDM6 KO) and PRDM6f/f mouse (Control) and compared the gene expression profile of the four groups of samples

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Human fetal yolk sac scRNA-seq data (sample ID: F158 for Haniffa Lab; 16099 for HDBR)

Project description:Investigating the blood, immune and stromal cells present in a human fetal embryo in a world first single cell transcriptomic atlas. The embryo was dissected into 12 coronal sections, yolk sac, and yolk sac stalk. Live single cells sorted, with cell suspension then undergoing 10x chromium 5 prime scRNA-seq. This accession contains the yolk sac and yolk sac stalk data from this embryo. A matched accession contains the coronal section data. Lane "WS_wEMB12142156" (from yolk sac) was excluded from downstream analysis due to low fraction reads in cells post-CellRanger QC. Termination procedure for this embryo was medical. The F158_[features...barcodes...matrix].[tsv...mtx].gz files attached to this accession represent raw count data from all the 10x lanes in this accession combined, and as output from CellRanger filtered matrices (CellRanger version 6.0.1 using human reference genome GRCh38-2020-A). One set of count matrices relates to the yolk sac data, and one set of count matrices relates to the yolk sac stalk data.

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