PRDM16 orchestrates neuron-vascular communication for angiogenesis during brain development
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ABSTRACT:
PROVIDER: PRJNA541483 | ENA |
REPOSITORIES: ENA
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Project description:Purpose:To gain a deeper insight into how PRDM16 regulates neuron-vascular communication for angiogenesis, RNA-sequencing (RNA-seq) was performed to analyze the genome-wide changes by PRDM16 deletion at E15. Methods: Total RNA was extracted from E15 telencephalic tissue of Prdm16cKO and Prdm16fl/fl mice. Then total RNA was quality controlled and quantified using an Agilent 2100 Bioanalyzer. After converting to cDNA and building library, high-throughput sequencing was performed using the Illumina HiSeq 2500 platform in Annoroad Genomics. Results: Approximately approximately one thousand transcripts showed differential expression between the Prdm16fl/fl and Prdm16cKO brain cortex, with a fold change ≥1.5 and p value <0.05. Gene ontology (GO) analysis showed that the down-regulated genes were enriched in the terms related to neurogenesis, blood vessel development and secretion by cells. Up-regulated genes showed a significant enrichment of terms involved in negative regulation of cell communication and negative regulation of angiogenesis. These results reflected the importance of PRDM16 in cortical development. Conclusions: We conclude that RNA-seq based transcriptome characterization would provide a framework for understanding how Prdm16 gene contribute to brain cortical development.
2019-05-08 | GSE130802 | GEO
Project description:Fli1+ cells transcriptional analysis reveals LMO2-PRDM16 axis in angiogenesis
| PRJNA627467 | ENA
Project description: Not available
| S-EPMC7370227 | biostudies-literature
Project description:Gene expression profile from brown adipose tissues of Prdm16 knockout and wile type mice. Prdm16 is a transcription factor that regulates the thermogenic gene program in brown and beige adipocytes. However, whether Prdm16 is required for the development or physiological function of brown adipose tissue (BAT) in vivo has been unclear. By analyzing mice that selectively lacked Prdm16 in the brown adipose lineage, we found that Prdm16 was dispensable for embryonic BAT development. Brown adipose tissues were collected from Prdm16 knockout and wiletype mice with 4 biological replicates per condition. Experiment was done in two separate batch for 6-week-old and 11-month-old. Extracted RNA was hybridized to Agilent two-color arrays.
2014-04-09 | E-GEOD-55080 | biostudies-arrayexpress
Project description:Mutation of the PRDM16 gene causes human dilated and noncompaction cardiomyopathy. The PRDM16 protein is a transcriptional regulator that affects cardiac development via Tbx5 and Hand1, thus regulating myocardial structure. The biallelic inactivation of Prdm16 induces severe cardiac dysfunction with postnatal lethality and hypertrophy in mice. The early pathological events that occur upon Prdm16 inactivation have not been explored. This study performed in-depth pathophysiological and molecular analyses of male and female Prdm16csp1/wt mice that carry systemic, monoallelic Prdm16 gene inactivation. We systematically assessed early molecular changes through transcriptomics, proteomics, and metabolomics. Kinetic modelling of cardiac metabolism was performed in silico with CARDIOKIN.
2023-07-21 | PXD043601 | Pride
Project description:Prdm16 is a transcription factor that drives a complete program of brown adipocyte differentiation, but the mechanism by which Prdm16 activates gene transcription remains unknown. Utilizing ChIP-seq teqhnique, we found that Prdm16 binds to chromatin at/near many brown fat-selective genes in BAT. Interestingly, Prdm16-deficiency dramatically reduced the binding of Med1 to Prdm16-target sites. Indeed, Prdm16 binds and recruits Med1 to BAT-enriched genes and the loss of Prdm16 caused a fundamental change in chromatin architecture at key BAT-selective genes and also reduced transcirptional activity. Moreover, Prdm16, through its interaction with Med1, defines and regulates the activity of super-enhancers that drive the expression of cell identity genes. Together, these data demonstrate that Prdm16 drives gene transcription by recruiting Med1 to control chromatin architecture and super-enhancers. Brown adipose tissues were collected from Prdm16 knockout and wiletype 9-month-old mice and ChIP-seq was performed for Prdm16, PolII, Med1, and H3K27ac.
2015-02-10 | E-GEOD-63965 | biostudies-arrayexpress
Project description:Group 1 -- WT or PRDM16-KO ex vivo murine MLL-AF9 cells, and PRDM16-KO AF9 cells overexpressing either f-PRDM16 or s-PRDM16. Group 2 -- WT or total PRDM16-KO murine HSCs isolated from adult BM. Group 3 -- WT or total PRDM16-KO murine HSCs isolated from fetal liver. Group 4 -- WT or f-PRDM16-KO murine HSCs (expressing s-PRDM16 only) isolated from fetal liver.
2018-06-08 | GSE112860 | GEO
Project description:PRDM16 ChIP was perfomed in control and Prdm16 KO crypts isolated from the duodenum of 6 week old mice 3 days after inducible gene deletion
2020-02-26 | GSE131487 | GEO
Project description:Purpose:To gain a deeper insight into how Prdm16 regulates cerebellar development, RNA-sequencing (RNA-seq) was performed to analyze the genome-wide changes by Prdm16 deletion at P3. Methods: Total RNA was extracted from P3 cerebellar tissue of Prdm16 cKO and Prdm16fl/fl mice. Then total RNA was quality controlled and quantified using an Agilent 2100 Bioanalyzer. After converting to cDNA and building library, high-throughput sequencing was performed using the Illumina HiSeq 2500 platform in Annoroad Genomics. Results: Approximately approximately one thousand transcripts showed differential expression between the Prdm16fl/fl and Prdm16 cKO cerebellum, with a fold change ≥1.5 and p value <0.05. Gene ontology (GO) analysis showed that the down-regulated genes were enriched in the terms related to regulation of glial cell differentiation and forebrain development, and cerebellum development. Up-regulated genes showed a significant enrichment of terms involved in negative regulation of cell differentiation. These results reflected the importance of Prdm16 in cerebellar development. Conclusions: We conclude that RNA-seq based transcriptome characterization would provide a framework for understanding how Prdm16 gene contribute to cerebellar development.
2019-07-11 | GSE134091 | GEO
Project description:PRDM16 is highly enriched in adult stem cells and plays a crucial role in multiple developmental processes. Here we demonstrate that PRDM16 is a histone H3K4 methyltransferase and this activity is essential for PRDM16 to function as a tumor suppressor. We show that PRDM16, through its regulation of transcription factor GFI1b, antagonizes the functions of MLL fusion proteins by repressing HOXA gene expression and therefore, specifically suppresses the transformation capability of MLL-AF9, MLL-AF6 and MLL-ENL. Furthermore, overexpression of PRDM16, but not the inactive PRDM16 mutant, blocks MLL mediated leukemogenesis while PRDM16 depletion significantly shortens the disease latency in vivo. We also show that PRDM16 activity is dynamically required at the pre-leukemic stage, but not in fully transformed leukemia, depicting a little known sequence of events necessary for clonal expansion during cancer evolution. Given the importance of PRDM16 and the loss of PRDM16 methyltransferase activity in an array of human malignancies, our findings provide broad insights for PRDM16-dependent physiological and pathological processes.
2016-12-15 | GSE64218 | GEO