New regulators of pluripotency and epigenetic reprogramming in ES and iPS cells

We are carrying out genome-wide epigenomics screens using state of the art array and Next Generation Sequencing (NGS) methods (MeDIP Seq, BS Seq, ChIP Seq and others). In collaboration with CellCentric and funding by TSB we have completed one such screen in which we identified 69 genes which are hypomethylated and expressed in ES cells while being hypermethylated and repressed in primary fibroblasts (pMEF) (Farthing et al 2008 PLoS Genet, Ng et al 2008 Nature Cell Biol). Likewise we identified 67 genes hypomethylated in TS cells and hypermethylated in pMEFs. Some of the genes that are expressed in ES and repressed in pMEFs are known regulators of pluripotency (eg Nanog) while others are of unknown function. Many of the gene candidates are suspected to have roles in transcriptional or epigenetic regulation. Our hypothesis is therefore that this gene set is enriched for new regulators of pluripotency and epigenetic reprogramming. Pluripotency in ES cells is maintained by a core circuitry of transcription factors which includes Oct4, Nanog, and Sox2. These transcription factors bind to a network of other genes which they either activate or repress. This must also include epigenetic reprogramming factors since ES cells are able to reprogramme somatic cells when they are fused to them, but the nature of these epigenetic modifiers is not known. Excitingly, a core set of four transcription factors (Oct4, Sox2, Klf4, c-myc) have been shown to be able to reprogramme pMEFs and other differentiated cell types to a pluripotent state (so called induced pluripotent stem, or iPS cells). Further work has shown that currently only two factors (either Oct4 and Klf4, or Oct4 and Sox2) in combination with drugs that affect epigenetic pathways (VPA affecting histone acetylation, BIX affecting histone methylation) are needed for induction of iPS cells, highlighting again the need for the induction of the pluripotency gene circuitry and that for epigenetic reprogramming of the genome. However, generation of iPS cells is a very inefficient process and many iPS lines are not completely epigenetically reprogrammed to a pluripotent state. The isolation of new pluripotency factors and epigenetic modifiers is therefore urgently needed in order to improve the prospects for the effective use of stem cells in regenerative medicine.