Deterministic Somatic Cell Reprogramming Involves Continuous Transcriptional Changes Governed by Myc and Epigenetic-Driven Modules

The epigenetic dynamics of induced pluripotent stem cell (iPSC) reprogramming in correctly reprogrammed cells at high resolution and throughout the entire process remain largely undefined. Here, we characterize conversion of mouse fibroblasts into iPSCs using Gatad2a-Mbd3/NuRD-depleted and highly efficient reprogramming systems. Unbiased high-resolution profiling of dynamic changes in levels of gene expression, chromatin engagement, DNA accessibility, and DNA methylation were obtained. We identified two distinct and synergistic transcriptional modules that dominate successful reprogramming, which are associated with cell identity and biosynthetic genes. The pluripotency module is governed by dynamic alterations in epigenetic modifications to promoters and binding by Oct4, Sox2, and Klf4, but not Myc. Early DNA demethylation at certain enhancers prospectively marks cells fated to reprogram. Myc activity drives expression of the essential biosynthetic module and is associated with optimized changes in tRNA codon usage. Our functional validations highlight interweaved epigenetic- and Myc-governed essential reconfigurations that rapidly commission and propel deterministic reprogramming toward naive pluripotency. [Display omitted] •Unbiased high-resolution profiling of mouse deterministic reprogramming to naive iPSCs•Early DNA demethylation of pluripotency enhancers definitively marks future iPSCs•Myc activity is indispensable for conducive iPS formation from somatic cells•Optimized changes in tRNA codon usage amplify the output of Myc governed program The epigenetic dynamics of iPSC reprogramming in correctly reprogrammed cells at high-resolution remain largely undefined. Hanna and colleagues now provide comprehensive characterization during the entire course of murine fibroblast reprogramming, by using Gatad2a-Mbd3/NuRD-depleted and radically efficient reprogramming systems. These data provide insights into key questions underlying successful naive iPSC reprogramming.