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EBF2 links KMT2D-mediated H3K4me1 to suppress pancreatic cancer progression via upregulating KLLN [RNA-seq]

ABSTRACT: We sought to elucidate the roles of KMT2D- and EBF2-regulated H3K4me1 in gene expression through profiling the gene transcription in PDAC cells overexpressed with EBF2 (EBF2-OE) or activated by GSK-LSD1, a selective inhibitor of KDM1A/LSD1 which can increase H3K4me1 level via blocking the histone H3K4 demethylase activity of KDM1A/LSD1

ORGANISM(S): Homo sapiens

PROVIDER: GSE237363 | GEO | 2023/07/18

REPOSITORIES: GEO

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EBF2 links KMT2D-mediated H3K4me1 to suppress pancreatic cancer progression via upregulating KLLN [Cut&Tag]

Project description:CUT-Tag revealed a strong reduction of KMT2D, H3K4me1 and EBF2 signals at the transcription start site (TSS) and promoter regions of genes that were downregulated in KMT2D-depleted (KMT2D-KD) cells

2023-07-18 | GSE237365 | GEO

EBF2 links KMT2D-mediated H3K4me1 to suppress pancreatic cancer progression via upregulating KLLN [ChIP-seq]

Project description:ChIP-seq revealed a strong reduction of KMT2D, H3K4me1 and EBF2 signals at the transcription start site (TSS) and promoter regions of genes that were downregulated in KMT2D-depleted (KMT2D-KD) cells

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EBF2 links KMT2D-mediated H3K4me1 to suppress pancreatic cancer progression via upregulating KLLN.

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-07-18 | GSE237366 | GEO

ChIP-sequencing of the H3K4me1/2 in crypts from mice intestinal epithelium with intestinal epithelium specific LSD1 knock out compared to wild type

Project description:To study the epigenetic regulation of intestinal epithelium we focus on the role of chromatin modulators. Lysine-specific histone demethylase 1a (KDM1A, LSD1) is one of the enzymes that can erase the H3K4me1/2 mark. To assess the role of LSD1 in intestinal epithelium we studied wild type (WT) (Villin-Cre -; Lsd1f/f) and intestinal-epithelial-specific knock-out (KO) (Villin-Cre+; Lsd1f/f) mice. We found that KO mice completely lack Paneth cells, and have altered stem cell characteristics compared to WT littermates. To assess genome-wide H3K4me1/2 levels in WT and KO small intestines, we sorted small intestinal crypt cells, fixed them, isolated chromatin, and performed ChIP using an H3K4me1 and an H3K4me2 antibody as described in the protocols.

2020-11-16 | E-MTAB-7871 | biostudies-arrayexpress

TAK-418-418, a LSD1 inhibitor, can rescue the genome wide chromatin abnormality in hippocapmus tissue in KMT2D+/bGeo mice after 2 week treatment [ChIP-seq]

Project description:KMT2D+/bGeoation in KMT2D, a histone-lysine N-methyl transferase, is responsible for majority of Kabuki syndrome in human. A mouse model of Kabuki syndrome with heterzygous KMT2D+/bGeoation of KMT2D, KMT2D+/bGeo was created to understand the disease mechanism and for drug discovery. TAK-418-418, a lysine-specific histone demethylase (LSD1) inhibitor, was tested on these mice for therapeutic treatment of the disease. Rescue of genome wide chromatin abnormality, which has been reported in KMT2D+/bGeo mice, was evaluated by high throughput next generation sequencing following chromatin immunoprecipitation of H3K4me1 and H3K4me3.

2020-03-11 | GSE146727 | GEO

H3K4me2 and gene expression profiling in control and KMT2D KD murine B220 cells

Project description:Define and compare H3K4me2 enrichment in murine B220 cells transduced with empty vector (ct) or KMT2D-shRNA. Compare gene expression by RNAseq in murine B220 cells transduced with empty vector (ct) or KMT2D-shRNA. Using H3K4me1/2 ChIPseq and RNAseq we profiled murine B220 purified cells from tumors transduced with EV (n=3) or KMT2D-shRNA (n=3).

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Genome-wide maps of chromatin state difference in KMT2D Knockdown/Control PC-3 Cells

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2018-10-23 | GSE94816 | GEO

Expression profiling of Ebf2- and Ebf2- stromal cells in mouse bone marrow

Project description:To identify the true molecular features of the Ebf2+ cells, we performed microarray analysis of freshly sorted CD45-TER119-Ebf2+ and Ebf2- cells. This allowed for the detection of 1968 genes that were 2-fold differentially expressed in Ebf2+ and Ebf2- cells. Among these, 1075 genes were upregulated and 893 genes including Ebf2, were downregulated in the Ebf2- as compared to the Ebf2+ cells. These include Nov, Fmod, Ndn, Dcn, Ctgf, Angiopoietin like-1(Angptl1), Fn1 and Jag1, some of which has been reported to be expressed in culture-selected MSCs. Furthermore, consistent with antigen expression analysis by FACS, the Ebf2+ cells highly expressed transcripts of Pdgfra, Pdgfrb, Sca1/Ly6a, Thy1 and Itga7 and Itgav, that have been suggested to be linked to MSCs. Nestin was mainly expressed in the Ebf2+ cells whereas it was hardly detectable in the Ebf2- cells. Altogether, molecularly, the Ebf2+ cells displayed features of a MSC. Ebf2 expression is not restricted to committed osteoblast progenitor cells but rather marks a multipotent mesenchymal progenitor cell population in adult mouse BM. These cells do not appear to be completely overlapping with the previous reported MSC populations. The findings provide new insights into the in vivo cellular identity and molecular properties of BM mesenchymal stem and progenitor cells.

2013-10-24 | GSE51608 | GEO

Expression profiling of Ebf2- and Ebf2- stromal cells in mouse bone marrow

2013-10-24 | E-GEOD-51608 | biostudies-arrayexpress

Ebf2-GFP in IEO cells

Project description:Comparison of Ebf2-expressing bone marrow mesenchymal cells from Ebf2-GFP heterozgous and Ebf2-GFP homozygous (=knock-out) mice

2017-12-17 | E-MTAB-2254 | biostudies-arrayexpress

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