STANDARD_NAME MIKKELSEN_PLURIPOTENT_STATE_UP SYSTEMATIC_NAME M1922 COLLECTION C2:CGP MSIGDB_URL https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/MIKKELSEN_PLURIPOTENT_STATE_UP NAMESPACE MOUSE_GENE_SYMBOL DESCRIPTION_BRIEF Genes up-regulated in the induced pluripotent cells (iPS) and embryonic stem cells (ES) compared to the parental lineage-committed and partially reprogrammed cell lines. DESCRIPTION_FULL Somatic cells can be reprogrammed to a pluripotent state through the ectopic expression of defined transcription factors. Understanding the mechanism and kinetics of this transformation may shed light on the nature of developmental potency and suggest strategies with improved efficiency or safety. Here we report an integrative genomic analysis of reprogramming of mouse fibroblasts and B lymphocytes. Lineage-committed cells show a complex response to the ectopic expression involving induction of genes downstream of individual reprogramming factors. Fully reprogrammed cells show gene expression and epigenetic states that are highly similar to embryonic stem cells. In contrast, stable partially reprogrammed cell lines show reactivation of a distinctive subset of stem-cell-related genes, incomplete repression of lineage-specifying transcription factors, and DNA hypermethylation at pluripotency-related loci. These observations suggest that some cells may become trapped in partially reprogrammed states owing to incomplete repression of transcription factors, and that DNA de-methylation is an inefficient step in the transition to pluripotency. We demonstrate that RNA inhibition of transcription factors can facilitate reprogramming, and that treatment with DNA methyltransferase inhibitors can improve the overall efficiency of the reprogramming process. PMID 18509334 GEOID GSE10781 AUTHORS Mikkelsen TS,Hanna J,Zhang X,Ku M,Wernig M,Schorderet P,Bernstein BE,Jaenisch R,Lander ES,Meissner A CONTRIBUTOR Jessica Robertson CONTRIBUTOR_ORG MSigDB Team EXACT_SOURCE Fig. 1: UP in iPS/ES FILTERED_BY_SIMILARITY EXTERNAL_NAMES_FOR_SIMILAR_TERMS EXTERNAL_DETAILS_URL SOURCE_MEMBERS Ash2l,Cbx7,Ccnb1,Dnmt3l,Dppa5,Lin28,Myst4,Nanog,Rex1,Suv39h2,Tdgf1 GENE_SYMBOLS ASH2L,CBX7,CCNB1,DNMT3L,DPPA5,LIN28A,KAT6B,NANOG,REXO1,SUV39H2,TDGF1 FOUNDER_NAMES