STANDARD_NAME	MIKKELSEN_MEF_LCP_WITH_H3K4ME3
SYSTEMATIC_NAME	MM840
COLLECTION	M2:CGP
MSIGDB_URL	https://www.gsea-msigdb.org/gsea/msigdb/mouse/geneset/MIKKELSEN_MEF_LCP_WITH_H3K4ME3
NAMESPACE	Mouse_RefSeq
DESCRIPTION_BRIEF	Genes with low-CpG-density promoters (LCP) bearing tri-methylation mark at H3K4 (H3K4me3) in MEF cells (embryonic fibroblasts).
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 & MEF=K4
FILTERED_BY_SIMILARITY	
EXTERNAL_NAMES_FOR_SIMILAR_TERMS	
EXTERNAL_DETAILS_URL	
SOURCE_MEMBERS	NM_001001602,NM_001003912,NM_001005475,NM_001012236,NM_001012324,NM_001013745,NM_001014761,NM_001033141,NM_001033249,NM_001033344,NM_001033345,NM_001033416,NM_001033669,NM_001033797,NM_001034060,NM_001037143,NM_001037713,NM_001039071,NM_001039072,NM_001039073,NM_001039074,NM_001039075,NM_001039076,NM_001039175,NM_001039176,NM_001042534,NM_001042611,NM_001045514,NM_001077362,NM_001081260,NM_001081394,NM_001082552,NM_007486,NM_007568,NM_007584,NM_007609,NM_007752,NM_007828,NM_007899,NM_008183,NM_008209,NM_008331,NM_008380,NM_008524,NM_008555,NM_008663,NM_008760,NM_008788,NM_008809,NM_008954,NM_009256,NM_009277,NM_009325,NM_009553,NM_009559,NM_009610,NM_009667,NM_009808,NM_009930,NM_009933,NM_010008,NM_010129,NM_010216,NM_010260,NM_010427,NM_010553,NM_010708,NM_010730,NM_010924,NM_011028,NM_011106,NM_011150,NM_011333,NM_011340,NM_011408,NM_011459,NM_011637,NM_011710,NM_011723,NM_011918,NM_011923,NM_013654,NM_015784,NM_016873,NM_018865,NM_019391,NM_019422,NM_019777,NM_020003,NM_021297,NM_021389,NM_021412,NM_022883,NM_022985,NM_022999,NM_023056,NM_025326,NM_025590,NM_025711,NM_025760,NM_025851,NM_027320,NM_027543,NM_027544,NM_027950,NM_028035,NM_028331,NM_029145,NM_029205,NM_029498,NM_031167,NM_032418,NM_032543,NM_033354,NM_053108,NM_053217,NM_078479,NM_130882,NM_133717,NM_133781,NM_133918,NM_134006,NM_134072,NM_134116,NM_134159,NM_138665,NM_144935,NM_145379,NM_145391,NM_145509,NM_146064,NM_153484,NM_153513,NM_153533,NM_172267,NM_172295,NM_172297,NM_172767,NM_172884,NM_172907,NM_172962,NM_175097,NM_175521,NM_177656,NM_177834,NM_178931,NM_198096
GENE_SYMBOLS	Dab2ip,Arhgef11,Iqsec2,Trex1,Ecm2,Zfp57,Scn2b,Ecscr,Zfp583,Styxl2,,Gal3st4,Fbxw10,G430095P16Rik,Rufy4,Pinlyp,Xaf1,Ldb3,Ldb3,Ldb3,Ldb3,Ldb3,Ldb3,Elovl1,Elovl1,Capg,Cp,Akna,Fhl1,Tnks1bp1,Tmem248,Trim21,Arhgdib,Btc,Ddr1,Casp4,Cp,Dapk3,Ecm1,Gstm2,Mr1,Ifit1,Inhba,Lum,Masp1,Myo7a,Ogn,Pcolce,Pdgfrb,Pspn,Serpinb9,Trim21,Tbxa2r,Zscan2,Zfp57,Actg2,Ampd3,Casp12,Col3a1,Col6a1,Cyp2j6,Emp3,Vegfd,Gbp2,Hgf,Il18rap,Lgals9,Anxa1,Nnmt,P2rx6,Pkig,Lgals3bp,Ccl2,Serpinf1,Slfn2,Serpinb8,Trex1,Wars1,Xdh,Ldb3,Angptl2,Ccl7,Postn,Ccn5,Ccn4,Lsp1,Elovl1,Ikbke,Glmp,Tlr4,Sh3kbp1,Mmp19,Lpin3,Zfand6,Prrg2,Tmem176b,Tmem176a,Acot11,Aspn,Hacd4,1700010I14Rik,Ifi35,Gpr173,Ggnbp1,Osgin1,Snx10,C1qtnf6,Rnase10,Spaca6,Zmym2,Il1rn,Dmpk,Rnf123,Sec16b,Glrx,Ifit1bl2,Mrps21,Cyp4f13,Rab43,Cab39,Emilin1,Rdh5,Akr1c14,Gpsm3,Il17rc,Sardh,Plppr2,Mrgprf,Tapbpl,Rab7b,Soat2,Tef,BC028528,Tns2,Phyhd1,Mab21l3,Ccdc9,Vwa5a,2900026A02Rik,Olfml1,Ddr1,Prickle3,Nyap1,6820408C15Rik,Cpa6,Tnfrsf14,Arap1
FOUNDER_NAMES