STANDARD_NAME MIKKELSEN_IPS_LCP_WITH_H3K4ME3 SYSTEMATIC_NAME M1975 COLLECTION C2:CGP MSIGDB_URL https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/MIKKELSEN_IPS_LCP_WITH_H3K4ME3 NAMESPACE Mouse_RefSeq DESCRIPTION_BRIEF Table 2S. Genes in MEF, MCV6, MCV8.1 and ES cells by epigenetic mark of their promoter 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 GSE11074 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 Table 2S: Promoter=LCP & MCV8.1=K4 FILTERED_BY_SIMILARITY EXTERNAL_NAMES_FOR_SIMILAR_TERMS EXTERNAL_DETAILS_URL SOURCE_MEMBERS NM_001001602,NM_001002794,NM_001003893,NM_001003912,NM_001004184,NM_001009573,NM_001012236,NM_001013384,NM_001013745,NM_001013814,NM_001014761,NM_001024145,NM_001033249,NM_001033315,NM_001033344,NM_001033345,NM_001033459,NM_001033669,NM_001033797,NM_001034060,NM_001034894,NM_001037143,NM_001037713,NM_001037915,NM_001038590,NM_001039114,NM_001039175,NM_001039176,NM_001042489,NM_001042534,NM_001080390,NM_001081028,NM_001081169,NM_001081260,NM_001081280,NM_001081291,NM_001081394,NM_001082552,NM_007491,NM_007655,NM_007828,NM_007955,NM_007976,NM_008034,NM_008183,NM_008230,NM_008340,NM_008433,NM_008600,NM_008713,NM_008788,NM_008809,NM_008952,NM_009151,NM_009277,NM_009291,NM_009553,NM_009559,NM_009710,NM_009853,NM_009944,NM_010008,NM_010129,NM_010168,NM_010197,NM_010292,NM_010575,NM_010686,NM_010734,NM_010767,NM_010929,NM_011011,NM_011012,NM_011028,NM_011193,NM_011281,NM_011355,NM_011452,NM_011637,NM_011710,NM_011850,NM_011923,NM_013514,NM_013545,NM_013561,NM_013591,NM_013605,NM_013631,NM_013658,NM_015766,NM_016754,NM_017461,NM_018876,NM_019412,NM_019422,NM_019789,NM_019798,NM_020003,NM_020286,NM_021327,NM_021610,NM_021791,NM_022320,NM_022880,NM_022985,NM_022999,NM_023517,NM_024283,NM_025330,NM_025590,NM_025760,NM_025771,NM_025851,NM_026205,NM_026296,NM_026316,NM_026415,NM_026690,NM_026820,NM_027165,NM_027320,NM_027543,NM_027544,NM_027658,NM_027890,NM_027988,NM_028035,NM_028064,NM_028752,NM_028783,NM_029498,NM_031393,NM_033606,NM_053108,NM_078479,NM_080639,NM_130882,NM_133781,NM_133903,NM_133918,NM_134116,NM_134159,NM_134251,NM_138583,NM_139232,NM_139234,NM_145226,NM_145391,NM_146026,NM_146064,NM_146198,NM_153086,NM_153105,NM_153127,NM_153484,NM_153508,NM_153513,NM_153533,NM_153577,NM_172267,NM_172295,NM_172542,NM_172767,NM_173365,NM_173427,NM_173772,NM_175097,NM_175367,NM_175521,NM_177123,NM_177158,NM_177376,NM_177656,NM_177697,NM_177788,NM_178260,NM_178444,NM_178650,NM_178656,NM_178747,NM_181344,NM_183131,NM_183278,NM_183424,NM_194059,NM_198048,NM_198096,NM_198618,NM_201366,NM_207202,NM_207265 GENE_SYMBOLS DAB2IP,,MASP2,ARHGEF11,SLC28A1,UNC13D,TREX1,PODNL1,ZFP57,AMT,SCN2B,PLA2G4F,ZNF583,HIPK4,STYXL2,,LRCOL1,FBXW10,,RUFY4,FOXR2,PINLYP,XAF1,RIPPLY1,CLDN19,ACSBG2,ELOVL1,ELOVL1,HVCN1,CAPG,MARK2,SIPA1L3,ASPG,TNKS1BP1,NLRC3,CCDC88B,TMEM248,TRIM21,ART5,CD79A,DAPK3,PTPRVP,F5,FOLR1,GSTM1,HDC,IGFALS,KCNN4,MIP,NOS3,PCOLCE,PDGFRB,PIPOX,SELPLG,TRIM21,STRA6,ZSCAN2,ZFP57,ART1,CD68,COX7A1,CYP2J2,EMP3,F2,FGF1,GCK,ITGA2B,LAPTM5,LST1,MASP2,NOTCH4,OPRK1,OPRL1,P2RX6,PSTPIP1,RORC,SPI1,SERPINB9,TREX1,WARS1,NR0B2,ANGPTL2,DMTN,PTPN6,HTR3A,MADCAM1,MUC1,PKLR,SEMA4A,EBI3,MYL11,SEPTIN1,FUT2,PRX,ELOVL1,KCNIP3,PDE4A,GLMP,TSPAN32,TNIP1,GPA33,DOC2GP,GPR35,SLC29A1,ZFAND6,PRRG2,TNFSF13,ECRG4,HSD17B14,ACOT11,HACD4,CNTNAP2,C6orf118,RNF151,CCDC121,ALDH3B1,CYSRT1,ASPDH,IFITM1,,IFI35,GPR173,GGNBP1,HEXIM2,SUSD2,NOXO1,SNX10,SLC39A4,HVCN1,ROBO4,ZMYM2,SYTL1,DQX1,GLRX,MRPS21,TIMP4,CYP4F3,CAB39,SPON2,EMILIN1,GPSM3,IL17RC,SLC12A8,TANGO2,FGD4,FGD4,OAS3,TAPBPL,PRR15L,SOAT2,SLC5A11,GJD4,CLDN19,MMRN2,TEF,CLSTN3,C1orf54,TNS2,SYNE4,PHYHD1,MAB21L3,ADAMTSL1,VWA5A,GPR20,KLHDC7A,NEU4,PRICKLE3,STON2,NYAP1,SPEF2,RINL,MYO3B,C20orf96,VWA3A,EXOC3L1,KISS1,EGFL7,TBC1D10C,PIRT,GULOP,C1RL,C16orf92,FAM25A,QRFP,NANOS3,PRX,ARAP1,DLGAP3,,CCDC120, FOUNDER_NAMES