Epigenetic resetting of human pluripotency

Recent attention has focussed on conversion of human pluripotent stem cells to a more naïve transcriptional and epigenetic status. Here we provide a simple method for resetting without transgenes via transient exposure to histone deacetylase inhibition. This protocol is effective across multiple embryo-derived and induced pluripotent stem cells. Reset cells can retain a normal karyotype over multiple passages. Specific markers and global transcriptome profile, including transposable element signature, diverge markedly from conventional human pluripotent stem cells and are consistent with a naïve-like identity. Global DNA methylation is reduced to a level similar to that reported for the inner cell mass, although gain of methylation is also apparent at certain loci. Imprinted methylation is mostly lost, however. In female cells, X chromosome reactivation is evidenced by bi-allelic transcription detected by RNA-FISH. XIST expression is also regained but is predominantly monoallelic. Reset cells are competent for tri-lineage differentiation, both via embryoid body formation and in adherent culture, and can also undergo germline specification. This reliable conversion system and associated transcriptome and methylome datasets will facilitate routine resetting for side by side evaluation with primed pluripotent stem cells and comprehensive interrogation and refinement of candidate naïve pluripotent stem cells. Overall design: BS-seq of conventional and reset human pluripotent stem cells