Figure 3
Bexarotene induces epigenetic changes in correlation with neuronal differentiation in ES cells.
ES cells were treated with 5 μM Bexarotene for 4 days and markers for neuronal differentiation were examined 6 days after plating (Day10, Neurons). Control cells were treated with vehicle and processed in the same way. (A) Outline of the protocol for ES cell treatment and differentiation. EBs, embryoid Bodies; (B) Genome browser view of lineage markers in ES cells for H3K4me3 identified by ChIP-seq at EBs stage or 4 days after bexarotene (Bexa, Day4) and vehicle (Veh, Day4) treatment. Note that for pluripotency markers Nanog and Oct4/Pou5f1 data are compared at EBs vs Bexa, Day4 and neuronal markers Pax6 and Syp are compared 4 days after bexarotene or vehicle treatment. (C) Bexarotene treatment increases the expression of Pax6 and Syp; (D) Comparative heatmap of significantly changed GO categories (gene lists derived from edgeR output tables) in APOE3 and APOE4 mice and epigenetic changes (analyzed ChIP-seq datasets) in bexarotene or vehicle treated ES cells (Day 4). Shown are the most significant distinct BP categories as determined by David in each experiment. Blue color indicates up-regulated genes and red indicates down-regulated genes in RNA-seq. For ChIP-seq data, Blue represents vehicle and red represents bexarotene. Gray boxes indicate no overlapping categories. Negative log10 (P value) denotes lower significance and red color higher significance; (E) Validation of RNA-seq results by qPCR in ES cells; Cells were treated with 5 μM bexarotene or vehicle for different time (24 h, Day 4 and Day 10). Values are mean ± SEM and statistics is by t-test; n = 3, *p < 0.05, **p < 0.01, ***p < 0.001.
