Role of the histone demethylase Kdm6b/Jmjd3 in somatic cell reprogramming [ATAC-Seq]

Somatic cells can be reprogrammed to pluripotent stem cells through the addition of just four transcription factors, OCT4, SOX2, KLF4 and c-MYC (OSKM). Although OSKM initiates reprogramming it is clear that extensive epigenetic remodeling is required to complete reprogramming. Critically, OSKM do not directly activate gene expression but instead recruit co-activators and co-repressors that remodel the local chromatin and in some way make the cells permissive for reprogramming. Consequently understanding how epigenetic co-repressors and co-activators are involved in reprogramming is a critical step in understanding the reprogramming process in detail. In this study we explored the role of the lysine-specific demethylase Kdm6b/Jmjd3 and its role in the reprogramming of somatic cells to pluripotent cells. ChIP-seq data consists of either input chromatin (MEF cells) or anti-H3K27me3 precipitated chromatin. Experiments were performed at three time points (MEFS, Day 5 and 10 of reprogramming cells) and in two MEF lines, one with Jmjd3wildtype and another with Jmjd3 Knockout. Additionally, either FLAG or Jmjd3 was overexpressed. The Jmjd3 knockout mice were a kind gift from Dr. Takashi Satoh (Takashi et al., 2010 Nat. Immunol.). ATAC-seq data was performed according to Buenrostro et al., 2015, on MEFs, ESCs, and Day 5 and day 10 OSKM-reprogramming cells