Genome-wide maps of the chromatin and transcription state transition during conversion from mouse embryonic fibroblasts (MEFs) to hepatocyte-like cells (iHep)

We have found three specific combinations of two transcription factors, comprising Hnf4alpha plus Foxa1, Foxa2, or Foxa3, could convert mouse embryonic fibroblasts (MEFs) into cells that closely resemble hepatocytes (iHep cells) in vitro. Then we mapped 2 histone modification marks (H3K9ac and H3K27me3) and 2 states of Pol2 (with phosphorylated serine 5 and phosphorylated both of serine 5 and serine 2) during the conversion event. Besides we performed FAIRE-Seq to explore the chromatin accessbility in the iHep cells. Overall design: ChIP-Seq for H3K9ac, H3K27me3, and Pol2 (with phosphorylated serine 5 and phosphorylated both of serine 5 and serine 2), and FAIRE-Seq in iHep_4a1 cells (Foxa1/Hnf4alpha), iHep_4a2 cells (Foxa2/Hnf4alpha), iHep_4a3 cells (Foxa3/Hnf4alpha), 3 cells 48 hours after transfection (48hr_4a1, 48hr_4a2, 48hr_4a3). ChIP-Seq for H3K9ac and H3K27me3 in MEF. ChIP-Seq for Pol2 in hepatocyte and a cell 48 hours after transfection of Foxa3 del2 mutant fused with x3 Ty1-tag and Hnf4alpha [iMEF(Day2)_4a3 del2_x3Ty1].