GSE135226
Oct4-mediated inhibition of Lsd1 activity promotes the active and primed state of pluripotency enhancers [methylRAD-seq]
Enhancer reactivation and pluripotency gene (PpG) expression could induce stemness and enhance tumorigenicity in cancer stem cells. Silencing of PpG enhancers (PpGe) during embryonic stem cell differentiation involves Lsd1–mediated H3K4me1 demethylation followed by DNA methylation. Here, we observed a widespread retention of H3K4me1 and DNA hypomethylation at PpGe associated with a partial repression of PpGs in F9 embryonal carcinoma cells (ECCs) post-differentiation. The absence of H3K4me1 demethylation could not be rescued by Lsd1 overexpression. Based on the observation that H3K4me1 demethylation is accompanied by strong Oct4 repression in P19 ECCs, we tested if Lsd1-Oct4 interaction affects Lsd1 catalytic activity. Our data show a dose-dependent inhibition of Lsd1 by Oct4 in vitro and retention of H3K4me1 at PpGe post-differentiation in Oct4 overexpressing P19 ECCs. These data suggest that Lsd1-Oct4 interaction in cancer stem cells may establish a primed enhancer state that is susceptible to reactivation leading to aberrant PpG expression. Overall design: To understand the mechanism by which cancer cells retain PpG expression, we investigated the mechanism of enhancer-mediated regulation of PpG expression in ECCs. This data correspond to genome-wide methylRAD sequencing experiment performed with undifferentiated (UD) and day four (D4) samples. Raw data is provided as FASTQ files. Processed data is provided as BedGraph files and TSV files. TSV files describe all methylated sites and columns are Chr, Sites, CgarType (cigar string – shows match, substitution, etc), count, and type of site (CCGG, CCAGG< or CCTGG).