Project description:Chromatin accessibility was assayed in wildtype or Dppa2 knockout ESC after 26 days of release of the trigger imposed by epigenetic editing. Samples were collected in two clonal knockout and wildtype lines after sorting at FACS of cells which maintained a repressive Esg1-tdTomato (TOMneg) reporter expression after 26 days of DOX washout (release of the trigger).
Project description:FACS purified cells from differentiation day 14-15 cells from 3 BAC transgenic mESC lines: Hes::GFP (early), Nurr1::GFP (mid), and Pitx3::YFP (late) DA neuron development reporter lines
Project description:FACS purified cells from differentiation day 14-15 cells from 3 BAC transgenic mESC lines: Hes::GFP (early), Nurr1::GFP (mid), and Pitx3::YFP (late) DA neuron development reporter lines All three lines were differentiated towards the midbrain dopamine phenotype, and FACS purification was performed at D14-15, and then subject to global transcriptome analysis
Project description:Early mammalian development entails widespread epigenome remodeling, including DNA methylation erasure and reacquisition, which facilitates developmental competence. To uncover the mechanisms that orchestrate global and focal DNA methylation (DNAme) dynamics, we coupled a single-cell ratiometric DNAme reporter with unbiased CRISPR screening. We identify key genes and regulatory pathways that drive developmental DNA hypomethylation, and characterise roles for Cop1 and Dusp6. We also identify Dppa2 and Dppa4 as essential safeguards of focal epigenetic states during (re)programming phases. In their absence, developmental genes and evolutionary young LINE1 elements lose H3K4me3 and gain ectopic de novo DNA methylation. Consequently, lineage-associated genes (and LINE1) acquire a repressive epigenetic memory in pluripotent cells, which renders them incompetent for activation during future lineage-specification. Dppa2/4 thereby sculpt a permissive epigenome for development by targeting H3K4me3 to counteract de novo methylation during (re)programming; a function that has been co-opted by evolutionary young LINE1 to evade epigenetic decommissioning.
Project description:Profiling of H3K4me1 genome wide occupancy in mESC WT, LSD1 KO, and rescued with WT LSD1 (RO) and with mutant LSD1 (AK) to explore the effects of LSD1 on histone methylation.
Project description:This SuperSeries is composed of the following subset Series: GSE31581: ECAT15-2/Dppa2 deficient ESCs GSE31582: ECAT15-2/Dppa2 transgenic rescue into ECAT15-2/Dppa2 deficient ESCs GSE31583: Lung of ECAT15-2/Dppa2 deficient embryo at E18.5 Refer to individual Series
Project description:RNA sequencing of FACS sorted microglia isolated from brain tissue of WT, Hexb-tdTomato, Hexb-CreERT2 and Hexb-KO mice was performed to test for potential differences in gene expression caused by the knock-in of tdTomato and CreERT2 into the Hexb locus.