Temporal resolution of global gene expression and DNA methylation changes in the final phases of reprogramming towards induced pluripotency.

Abstract

The generation of induced pluripotent stem cells (iPSCs) involves activation of the endogenous pluripotency circuitry and global DNA demethylation late in reprogramming, but temporal resolution of these events using existing markers is insufficient. Here, we generated murine transgenic lines harboring dual fluorescent reporters reflecting cell-state specific expression of the master pluripotency factor Oct4 and the 5-methylcytosine dioxygenase Tet1. By assessing reprogramming intermediates based on dual reporter patterns, we identified a sequential order of Tet1 and Oct4 gene activation at proximal and distal regulatory elements following pluripotency entry. Full induction of Tet1 marks a pivotal late intermediate stage occurring after a phase of global gene repression, and preceding full activation of Oct4 along with late naive pluripotency and germline-specific genes. Sequential activation of Tet1 further distinguishes two waves of global DNA demethylation, targeting distinct genomic features and largely uncoupled from transcriptional changes, with dynamics unique to iPSC reprogramming. Moreover, we demonstrate that loss of Tet1 is compatible with reprogramming towards full Oct4 gene activation, but generates iPSCs with aberrant DNA methylation, chromosomal instability during lineage priming and defective differentiation potential. Therefore, the transcriptional logic of Tet1 expression signals a deterministic epigenetic roadmap towards generation of high quality iPSCs.