Genome-wide multiple omics characterization of somatic cell reprogramming. Mus musculus strain:CD1 X 129/S2 X C57/B6

Transcription factor-driven somatic cell reprogramming to induced pluripotent stem cells (iPSCs) reshapes the global genetic, epigenetic, and transcriptional landscapes of cells to achieve pluripotency. As an international consortium, we conducted a massive parallel screen (“Project Grandiose”) using next generation sequencing to profile the transcriptome (microRNA, lncRNA (long non-coding RNA) and mRNA), epigenome (chromatin marks: H3K4me3, H3K27me3 and H3K36me3) of reprogramming cells. Samples were collected at specific time points during reprogramming of an inducible secondary mouse embryonic fibroblasts towards iPS cells. Our study provides the molecular profile of multiple reprogramming and pluripotent states that are defined by widespread changes in chromatin state and specific coding and non-coding gene transcriptional signatures. The dynamics of H3K27me3 drive early events during reprogramming and promote a transient open/primed chromatin state near key developmental regulators. When high transgene expression is maintained, H3K27me3 is re-acquired and reprogramming cells stabilize but completely deviate from the iPSC fate, although they maintain an alternate stable state. Lowering transgene expression during this state drives the cells closer to iPSCs. Furthermore, acquisition of iPSC-like chromatin marks is achieved late in reprogramming, including gain of bivalent chromatin. Our data provide panoramic insight into the mechanisms of transgene driven reprogramming, highlighting the role of specific gene expression networks and their genomic and epigenetic underpinnings.