Role of the histone demethylase Kdm6b/Jmjd3 in somatic cell reprogramming [RNA-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. RNA-seq data consists of MEFs at passage 2 or 4, with or withour JMJD3 overexpression, and reprogrammed cells with the ectopic expression of OSKM (Oct4, Sox2, Klf4, c-Myc), along with either control transfections (FLAG, shLuc) or JMJD3 overexpression or Jmjd3 or Utx knockdown. Two time points in the reprogramming time course were profiled: Day 4 (early) and Day 8 (late)