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Effect of depletion of histone demethylases KDM6A and KDM6B on gene expression in the acute myeloid leukemia (AML) cell line U937 [RNA-seq]

ABSTRACT: To investigate the function of KDM6A and KDM6B in regulating gene expression in AML, we generated U937 cell lines having knockdown of either KDM6A, KDM6B or both using lentiviral shRNA. Control cells were generated using a scrambled shRNA. We then profiled gene expression using RNA-seq data obtained from the 3 knockdown cell lines compared with the control cell line.

ORGANISM(S): Homo sapiens

PROVIDER: GSE223609 | GEO | 2023/01/29

REPOSITORIES: GEO

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Decoding changes in chromatin accessibility mediated by KDM6 histone demethylases [ATAC-seq]

Project description:To interrogate the function of KDM6A and KDM6B in regulating genome accessibility, we generated U937 cell lines having knockdown of either KDM6A, KDM6B or both using lentiviral shRNA. We then profiled chromatin accessibility changes using ATAC-seq data obtained from the 3 knockdown cell lines compared with the wild type cell line.

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Refractory testicular germ cell tumors are highly sensitive to the targeting of polycomb pathway demethylases KDM6A and KDM6B

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The histone lysine demethylase Kdm6b is required for activity-dependent preconditioning of hippocampal neuronal survival

Project description:We profiled basal and bicuculline+4-AP inducible mRNA expression in cultured mouse hippocampal neurons with or without viral shRNA mediated knockdown of Kdm6b We harvested mRNA from neurons under four conditions (pLKO vector/treatment control, pLKO vector/3hr bicuculline+4AP, Kdm6b knockdown/treatment control,Kdm6b knockdown/3hr bicuculline+4AP). Libraries were generated and used for RNA sequencing.

2014-06-12 | E-GEOD-58398 | biostudies-arrayexpress

Effect of depletion of histone demethylases KDM6A and KDM6B on gene expression in the acute myeloid leukemia (AML) cell line U937 [RNA-seq]

Project description:Effect of depletion of histone demethylases KDM6A and KDM6B on gene expression in the acute myeloid leukemia (AML) cell line U937 [RNA-seq]

| PRJNA926974 | ENA

The histone lysine demethylase Kdm6b is required for activity-dependent preconditioning of hippocampal neuronal survival

Project description:We profiled basal and bicuculline+4-AP inducible mRNA expression in cultured mouse hippocampal neurons with or without viral shRNA mediated knockdown of Kdm6b

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H3K27me3 demethylases maintain the transcriptional and epigenomic landscape of the intestinal epithelium [CHIP-seq]

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2022-12-31 | GSE200975 | GEO

H3K27me3 demethylases maintain the transcriptional and epigenomic landscape of the intestinal epithelium [RNA-seq]

2022-12-31 | GSE200974 | GEO

KDM4B- and KDM6B-regulated genes in human mesenchymal stem cell osteogenic differentiation

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Project description:Recent studies have delineated cancer type-specific roles of histone 3 lysine 27 (H3K27) demethylase KDM6B/JMJD3 depending on its H3K27 demethylase activity. Here we show that KDM6B is expressed in multiple myeloma (MM); and that shRNA-mediated knockdown and CRISPR-mediated knockout of KDM6B abrogate MM cell growth and survival. TNFα or bone marrow stromal cell culture supernatants induce KDM6B, which is blocked by IKKβ inhibitor MLN120B, suggesting KDM6B is regulated by NF-κB signaling in MM cells. RNA-sequencing and subsequent ChIP-qPCR analyses reveal that KDM6B is recruited to the loci of genes encoding components of MAPK signaling pathway including ELK1 and FOS, and upregulates these genes expression without affecting H3K27 methylation level. Overexpression of catalytically-inactive KDM6B activates expression of MAPK pathway-related genes, confirming its function independent of demethylase activity. We further demonstrate that downstream targets of KDM6B, ELK1 and FOS, confer MM cell growth. Our study therefore delineates KDM6B function that links NF-κB and MAPK signaling pathway mediating MM cell growth and survival, and validates KDM6B as a novel therapeutic target in MM.

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Gene expression changes upon knockdown of DEK in the U937 cell line

Project description:Gene expression profiling of U937 cells upon knockdown of the DEK oncogene by two different shRNAs (shDEK14 and shDEK17). The DEK oncogene was knocked down by shRNA to study the changes in gene expression.

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