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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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RNA-seq of murine Th1 and Th2 cells differentiated for 24hr with or without the presence of actin and EZH2 inhibitors

ABSTRACT: CD4 T helper cells can differentiate to several types of cells like Th1, Th2, Th17 and Treg. This process is directed by cytokines and activation of T cells by specific antigens. This process has its own plasticity and it is directed by epigenetic changes allowing cells to develop and differentiate. In this experiment, we wanted to explore if EZH2 has a transcriptional regulation in the first day of differentiation. To study this we performed RNA-seq with or without UNC1999, an EZH2 inhibitor. Moreover, we wanted to learn the interaction between EZH2 and nuclear Actin, so Cytochalasin B was added to look for similar transcriptional pattern.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Mus musculus

SUBMITTER: Yiftah Barsheshet

PROVIDER: E-MTAB-9523 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Chip-seq of EZH2 and VAV1 in 24hr differentiated Th1 and Th2 cells with or without EZH2 or Actin polymerization inhibitors

Project description:CD4 T helper cells can differentiate to several types of cells like Th1, Th2, Th17 and Treg. This process is directed by cytokines and activation of T cells by specific antigens. This process has its own plasticity and it is directed by epigenetic changes allowing cells to develop and differentiate. In this experiment, we wanted to explore the binding pattern of EZH2 in the first 24 hours of Th cells activation and differentiation side by side with VAV1 binding pattern to understand the importance of actin polymerization factors in this process.

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An Ezh2 and Ezh1 dual inhibitor, UNC1999, re-shapes the landscape of H3K27me3 versus H3K27ac in MLL-AF9-transformed murine leukemia

Project description:Ezh2 and EZH1 are histone H3 lysine 27 (H3K27)-specific methyltransferases. Their hyperactive mutations and overexpression were found in cancer including various hematological malignancies. UNC1999 is a highly selective inhibitor for both enzymes. It suppresses H3K27 tri- and di-methylation globally and inhibits growth of MLL-rearranged acute leukemia. Here we performed ChIP-Seq to profile how UNC1999 affects distribution of H3K27me3 and its antagonizing H3K27ac in MLL-AF9-immortalized leukemia cells. We also performed ChIP-seq of SUZ12, an essential common cofactor of EZH2 and EZH1 following compound treatments. We treated MLL-AF9 transformed murine leukemia cells with DMSO, UNC1999 or UNC2400 (an inactive analog compound of UNC1999). Cells were then collected and used for ChIP-Sequencing of Input, H3K27me3, SUZ12, and H3K27ac.

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An Ezh2 and Ezh1 dual inhibitor, UNC1999, re-shapes the landscape of H3K27me3 versus H3K27ac in MLL-AF9-transformed murine leukemia

2014-10-30 | GSE62437 | GEO

Expression data of MLL-AF9-transformed murine leukemia progenitor cells, following treatment with UNC1999, a dual Ezh1 and Ezh2 inhibitor, or knockdown of EED

Project description:Ezh2 and EZH1 are histone H3 lysine 27 specific methyltransferase. Their hyperactive mutations and overexpression were found in cancer including various hematological malignancies. UNC1999 is a highly selective inhibitor for both enzymes. It suppresses H3K27 tri- and di-methylation globally and inhibits growth of MLL-rearranged acute leukemia cell lines. UNC2400, a di-methylated derivative of UNC1999, is employed an inactive analog compound for assessment of off-target effects. EED knockdown was used to demonstrate gene targets of PRC2. Here we performed microarray analysis in MLL-AF9 transformed acute leukemia cells following treatment with DMSO, UNC2400 or UNC1999, or after induction of EED shRNA (Renilla shRNA as control). This study allows us to identify UNC1999-responsive gene signatures as well as their overlap with PRC2 targets in MLL-AF9-bearing leukemia cells. We analyzed 5 of DMSO-treated, 5 of UNC2400 (inactive analog of UN1999)-treated, and 6 of UNC1999-treated MLL-AF9 leukemia cell samples to identify UNC1999-responsive gene signatures. We also performed microarray in 3 of shRNA control lines (Renilla or Ren) and 3 of shEED lines to identify downstream targets of PRC2 complex in MLL-AF9 leukemia cells.

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Expression data of MLL-AF9-transformed murine leukemia progenitor cells, following treatment with UNC1999, a dual Ezh1 and Ezh2 inhibitor, or knockdown of EED

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Investigation of bivalently marked promoters in patient-derived colorectal cancer stem cells by ChIP-seq, chromatin accessibility by ATAC-seq, and differential regulation of gene expression following EZH2 inhibition using RNA-seq.

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