IBET JMJD6
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB49820 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR7910350.fastq.gz | Fastqsanger.gz | |||
| ERR7910350_1.fastq.gz | Fastqsanger.gz | |||
| ERR7910350_2.fastq.gz | Fastqsanger.gz | |||
| ERR7910360.fastq.gz | Fastqsanger.gz | |||
| ERR7910360_1.fastq.gz | Fastqsanger.gz |
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Project description:By survival analysis of breast cancer patients, JMJD6 was found to be significantly associated with poor prognosis. Over-expression and knock-down of JMJD6 in breast cancer cell lines suggested a role in proliferation. In order to study the transcriptional events that occur following JMJD6 expression changes, siRNA-mediated knock-down of JMJD6 was performed in MCF-7 and MDA-MB231 and stable over-expression of JMJD6 was performed in MCF-7. There are 2 different siRNA-mediated knock-downs of JMJD6 with 2 biological replicates in MCF-7 and MDA-MB231; 3 clones of JMJD6 over-expression with 3 biological replicates in MCF-7. The control for the knock-downs is scrambled siRNA-treated MCF-7 and MDA-MB231 and the control for JMJD6 over-expression is empty vector over-expression in MCF-7.
2012-05-09 | E-GEOD-31782 | biostudies-arrayexpress
Project description:By survival analysis of breast cancer patients, JMJD6 was found to be significantly associated with poor prognosis. Over-expression and knock-down of JMJD6 in breast cancer cell lines suggested a role in proliferation. In order to study the transcriptional events that occur following JMJD6 expression changes, siRNA-mediated knock-down of JMJD6 was performed in MCF-7 and MDA-MB231 and stable over-expression of JMJD6 was performed in MCF-7.
2012-05-10 | GSE31782 | GEO
Project description:Clear cell renal cell carcinoma (ccRCC) represents a lethal disease and classically resistant to cytotoxic chemotherapy, highlighting the importance of identifying new therapeutic vulnerabilities. We performed a functional siRNA screening for all 2-oxoglutarate (2-OG)-dependent enzymes in ccRCC using 3-D soft agar colony formation assay, and combined with TCGA data, we identified Jumonji domain-containing 6 (JMJD6) as an essential gene for ccRCC tumorigenesis. Downregulation of JMJD6 abolished ccRCC colony formation in vitro and inhibited orthotopic tumor growth in vivo. Integrated analyses of ChIP-seq and RNA-seq identified that JMJD6 can transcriptionally regulate the expression of diacylglycerol O-acyltransferase 1 (DGAT1) by co-occupying the target gene promoter with H3K4me3. Downregulation of JMJD6 caused decreased expression of DGAT1 at both mRNA and protein level. Inhibition or depletion of DGAT1 induced decreased cell growth in vitro or inhibited tumor growth in vivo. Mechanistically, decreased DGAT1 caused decreased LD formation in ccRCC, while restoration of JMJD6 expression can restore DGAT1 level, and LD formation as well as cell growth. In summary, JMJD6 is essential for ccRCC lipid storage and tumorigenesis through a DGAT1-dependent signaling. Therefore, the JMJD6-DGAT1 axis serves as a potential therapeutic avenue for ccRCC.
2022-06-27 | GSE182888 | GEO
Project description:Association of Jumonji domain-containing 6 (JMJD6) with outcomes of various cancers has been shown, however the impact on intrahepatic cholangiocarcinoma (ICC) has never been reported yet. The aim of this study is to clarify the role of JMJD6 in the clinical settings and the impact on the outcomes of ICC. The resected liver specimens of 53 patients who underwent surgery for ICC were analyzed for JMJD6 expression by immunohistochemistry staining. The relationship between clinicopathological factors and the JMJD6 expression was investigated. Commercial culture cell lines derived from primary ICC were incubated with siRNA to decrease the expression of JMJD6. The RNA and protein were extracted to analyze the downstream gene expression with RNA-sequence and western blotting. The relationship between JMJD6 expression and tumor immunological factors were evaluated. Low expression of JMJD6 was significantly associated with poor overall survival (OS, p=0.0024). The further analyses revealed that the higher expression of JMJD6 was one of the independent better prognostic factors. ICC cells with JMJD6 knockdown revealed significantly higher programmed death-ligand 1 (PD-L1) expression (p=0.0410) in RNA-seq. The western blotting showed the result matching with the RNA-seq. H3K4me3 histone protein expression was also upregulated under the knockdown of JMJD6. A higher CD8+ T cell count combined with high expression of JMJD6 was one of the significant indicators of better prognosis both in PFS and OS. In vitro experiments proved that JMJD6 regulated the expression of PD-L1 and the paired evaluation of JMJD6 and the immune status was one of the useful factors to stratify the prognosis of ICC. Our results suggest that JMJD6 could influence the prognosis of ICC through the epigenetic regulation of PD-L1 expression.
2022-03-23 | GSE171974 | GEO
Project description:The Jumonji domaining-containing protein JMJD6 is a 2-oxoglutarate dependent dioxygenase that has been implicated in a broad range of biological functions. Cellular studies have implicated the enzyme in chromatin biology, transcription, DNA repair, mRNA splicing and co-transcriptional processing. Although not all studies agree, JMJD6 has been reported to catalyse both hydroxylation of lysine residues and demethylation of arginine residues. However, despite extensive study and the indirect implication of JMJD6 catalysis in many cellular processes, direct assignment of JMJD6 catalytic substrates has been limited. Examination of a site of reported prolyl hydroxylation within a lysine-rich region of the bromodomain protein BRD4 led us to conclude that hydroxylation was in fact on lysine and catalysed by Jmjd6. This prompted a wider search for JMJD6-catalysed protein modifications deploying mass spectrometric methods designed to identify novel substrate associations and facilitate analysis of lysine-rich regions by LC-MSMS. Using derivatization of lysine with propionic anhydride to improve the analysis of tryptic peptides and a pharmacological inhibitor of JMJD6 to stabilise enzyme/substrate associations, we report over 100 sites of JMJD6-catalysed lysyl hydroxylation on 48 protein substrates including 19 sites of hydroxylation on BRD4. Most hydroxylations were within lysine-rich regions that are predicted to be unstructured; in some multiple modifications were observed on adjacent lysine residues. Almost all of the JMJD6 substrates defined in this study have been associated with membraneless organelle formation. Taken together with findings implicating lysine-rich regions in subcellular partitioning by liquid-liquid phase separation, our findings raise the possibility that JMJD6 may play a role in regulating such processes in response to stresses, including hypoxia. Note, this dataset corresponds to Figure 3 of the published manuscript; which employs a substrate-trapping methodology to identify novel substrates of JMJD6 by label free DIA approach.
2022-08-02 | PXD031155 | Pride
Project description:Human umbilical vein endothelial cells (HUVECs) were incubated for 48 h after transfection of scrambled siRNA or siRNA targeting Jmjd6 . Changes in transcript and exon levels were analyzed.
2012-05-04 | GSE37741 | GEO
Project description:Human umbilical vein endothelial cells (HUVECs) were incubated for 48 h after transfection of scrambled siRNA or siRNA targeting Jmjd6 . Changes in transcript and exon levels were analyzed. 6 samples; 2 conditions: Scrambled siRNA vs. siJmjd6 ; 3 replicates per condition
2012-05-03 | E-GEOD-37741 | biostudies-arrayexpress
Project description:<p>The purpose of this study was to obtain tissue specimens derived from patients with melanoma to generate research tools to advance our understanding of the genetics, pathogenesis, and therapeutics of melanoma. Briefly, tissue was obtained from metastatic lesions and used to generate clonal primary cell lines from melanoma cells and fibroblasts from the tumor microenvironment. RNA was extracted from low passage cell lines using Trizol reagent. cDNA libraries were prepared using the TruSeq mRNA sample preparation kit, v2 (Illumina) and sequenced on the HiSeq 2000 platform (Illumina). The submitted files are bam files that contain both unaligned and aligned reads (human genome, build hg19). </p>
| phs001115 | dbGaP
Project description:Emerging evidence suggests Jumonji domain-containing proteins are epigenetic regulators in diverse biological processes including cellular differentiation and proliferation. RNA interference-based analyses combined with gene expression profiling can effectively characterize the cellular functions of these enzymes. We found that the depletion of Jumonji domain-containing protein 6 (Jmjd6) and its paralog protein Jumonji domain-containing protein 4 (Jmjd4) individually by small hairpin RNAs (shRNAs) slowed cell proliferation of mouse NIH3T3 fibroblasts. We subsequently performed gene expression profiling on both Jmjd6- and Jmjd4-depleted mouse NIH3T3 fibroblasts using the Affymetrix GeneChip Mouse Exon 1.0 ST Array. We anaylzed control shRNA-treated cells, Jmjd6- and Jmjd4- depleted cells using Affymetrix Mouse Exon 1.0 ST platform. Two biological replicates were performed (total 6 samples). Array data was processed by Affymetrix Expression Console.
2016-01-12 | E-GEOD-76758 | biostudies-arrayexpress
Project description:The Jumonji domaining-containing protein JMJD6 is a 2-oxoglutarate dependent dioxygenase that has been implicated in a broad range of biological functions. Cellular studies have implicated the enzyme in chromatin biology, transcription, DNA repair, mRNA splicing and co-transcriptional processing. Although not all studies agree, JMJD6 has been reported to catalyse both hydroxylation of lysine residues and demethylation of arginine residues. However, despite extensive study and the indirect implication of JMJD6 catalysis in many cellular processes, direct assignment of JMJD6 catalytic substrates has been limited. Examination of a site of reported prolyl hydroxylation within a lysine-rich region of the bromodomain protein BRD4 led us to conclude that hydroxylation was in fact on lysine and catalysed by Jmjd6. This prompted a wider search for JMJD6-catalysed protein modifications deploying mass spectrometric methods designed to identify novel substrate associations and facilitate analysis of lysine-rich regions by LC-MSMS. Using derivatization of lysine with propionic anhydride to improve the analysis of tryptic peptides and a pharmacological inhibitor of JMJD6 to stabilise enzyme/substrate associations, we report over 100 sites of JMJD6-catalysed lysyl hydroxylation on 48 protein substrates including 19 sites of hydroxylation on BRD4. Most hydroxylations were within lysine-rich regions that are predicted to be unstructured; in some multiple modifications were observed on adjacent lysine residues. Almost all of the JMJD6 substrates defined in this study have been associated with membraneless organelle formation. Taken together with findings implicating lysine-rich regions in subcellular partitioning by liquid-liquid phase separation, our findings raise the possibility that JMJD6 may play a role in regulating such processes in response to stresses, including hypoxia. This deposition contains all hydroxylysine assignment data.
2022-08-02 | PXD031221 | Pride