STANDARD_NAME MIKKELSEN_NPC_HCP_WITH_H3K27ME3 SYSTEMATIC_NAME M2009 COLLECTION C2:CGP MSIGDB_URL https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/MIKKELSEN_NPC_HCP_WITH_H3K27ME3 NAMESPACE MOUSE_GENE_SYMBOL DESCRIPTION_BRIEF Genes with high-CpG-density promoters (HCP) bearing histone H3 trimethylation mark at K27 (H3K27me3) in neural progenitor cells (NPC). DESCRIPTION_FULL We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic stem cells, neural progenitor cells and embryonic fibroblasts. We find that lysine 4 and lysine 27 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential. Lysine 36 trimethylation marks primary coding and non-coding transcripts, facilitating gene annotation. Trimethylation of lysine 9 and lysine 20 is detected at satellite, telomeric and active long-terminal repeats, and can spread into proximal unique sequences. Lysine 4 and lysine 9 trimethylation marks imprinting control regions. Finally, we show that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations. PMID 17603471 GEOID GSE12241 AUTHORS Mikkelsen TS,Ku M,Jaffe DB,Issac B,Lieberman E,Giannoukos G,Alvarez P,Brockman W,Kim TK,Koche RP,Lee W,Mendenhall E,O'Donovan A,Presser A,Russ C,Xie X,Meissner A,Wernig M,Jaenisch R,Nusbaum C,Lander ES,Bernstein BE CONTRIBUTOR Arthur Liberzon CONTRIBUTOR_ORG MSigDB Team EXACT_SOURCE Table 4S: Class=HCP & NPC state=K27 FILTERED_BY_SIMILARITY EXTERNAL_NAMES_FOR_SIMILAR_TERMS EXTERNAL_DETAILS_URL SOURCE_MEMBERS 0710005M24Rik,1700001C19Rik,2310031A18Rik,2610019F03Rik,2810405K02Rik,4831426I19Rik,4931429I11Rik,6330514A18Rik,A330008L17Rik,A830041P22Rik,A930034L06Rik,Abcg1,Adra2c,AI427515,AI595406,AI661453,Aldh1a2,Alk,Alx3,Amigo2,Ankrd56,Atp12a,Atp2b2,B3gnt7,B4galnt2,Bai1,BC004853,BC021891,BC062109,BC065085,Bcl11a,Bhlhb4,Bmp4,Bmp6,Bnc1,Bnc2,C1ql1,C1ql2,C1qtnf4,C630035N08Rik,C79127,Cabp7,Cacna2d2,Cadm3,Calcr,Car10,Car7,Cart1,Cartpt,Cbln4,Cckbr,Cdh1,Cdh8,Cdx2,Celsr1,Chat,Chrna4,Cldn7,Clstn2,Cnnm1,Cntn2,Cobl,Col13a1,Col14a1,Col15a1,Colec12,Cplx1,Cpne5,Cpz,Crb3,Crhr1,Crtac1,Cryba2,Cxcl14,Cyp26a1,Cyp2s1,D11Bwg0517e,D5Ertd593e,D930020B18Rik,Dact2,Dbx1,Degs2,Dlgap2,Dlx3,Dmbx1,Dmrt1,Dmrt2,Dmrt3,Dock8,Dpp10,Drd2,Dscaml1,E130309D14Rik,Ecel1,Edg8,Eif4e3,Emx1,Epha8,Evx1,Evx2,Fev,Fezf2,Fgf14,Fgf3,Fgf4,Fibcd1,Flt3,Foxb2,Foxd3,Foxe3,Foxg1,Foxl1,Foxn4,Fstl4,Gabra5,Gabrg3,Galnt13,Galr3,Garnl4,Gata5,Gfi1,Ghsr,Gja9,Gjb2,Gm1337,Gm691,Gm879,Gm996,Gpr120,Gpr27,Gpr37,Grik3,Grin1,Grin2b,Grm7,Gsh1,Gsh2,Hck,Hcn1,Hcn2,Hcrtr1,Hecw1,Hes2,Hoxa11,Hoxa13,Hoxa9,Hoxb1,Hoxb2,Hoxb3,Hoxb4,Hoxb5,Hoxb7,Hoxb8,Hoxb9,Hoxc10,Hoxc13,Hoxc6,Hoxc8,Hoxc9,Hoxd10,Hoxd11,Hoxd9,Hpcal4,Hr,Hrh3,Hs3st6,Htr1a,Htr7,Igf2,Igf2bp1,Igfbpl1,Igsf21,Ihh,Ikzf1,Ikzf3,Il11,Iqsec3,Irf5,Isl1,Jag2,Jph3,Kcna7,Kcnh1,Kcnk3,Kcnk6,Kcnq1,Kcnq2,Kcns2,Kcns3,Kctd8,Lad1,Lbx1,Lbxcor1,Lemd1,Lhx5,Lhx8,Lin28,Lipg,Llgl2,Lmx1a,LOC625638,Lrat,Lrfn5,Lsr,Ltbp2,Ly6h,Mal,Mal2,Mast1,Mesp1,Mixl1,Mpped1,Msc,N28178,Nefh,Nell1,Neurod2,Neurog3,Nfatc2,Nkx2-3,Nkx6-1,Nlrp6,Npas1,Npas2,Npr3,Nptxr,Nxph2,Onecut3,Oprd1,Otop1,Otp,Ovol1,Ovol2,P140,Pappa,Pax1,Pax3,Pax7,Pdgfb,Pdx1,Penk1,Pgbd5,Pgr,Phlda2,Pitpnm3,Pitx1,Plxdc1,Pou2f3,Pou4f2,Pou4f3,Ppp2r2c,Prdm16,Prkcz,Prok2,Prokr2,Prph1,Ptf1a,Pthr1,Ptprn,Ptprt,Pyy,Rab11fip1,Rab11fip4,Rab37,Rasgef1c,Ripk4,Rprml,Rspo1,Rtn4r,Rxrg,Ryr2,Sall4,Scn4b,Scn5a,Scnn1g,Scrt1,Scube1,Serinc2,Sfrp1,Sfrp5,Sgpp2,Sigirr,Sim1,Sim2,Six6,Skap1,Slc12a5,Slc17a6,Slc22a3,Slc30a3,Slc38a4,Slc6a17,Slc6a3,Slc6a5,Slc7a14,Slc9a2,Slco4c1,Slit2,Snai3,Sorcs3,Sox18,Sp8,Spint1,Spnb3,St8sia3,St8sia6,Stac2,Stmn2,Sult4a1,Syt12,Syt2,T,Tbx21,Tbx3,Tcerg1l,Tcf15,Tcfap2b,Tcfap2c,Tcfap2d,Titf1,Tlx1,Tlx3,Tmem130,Tmem132e,Tmem151,Tmem163,Tmem166,Tmem28,Tnfrsf11a,Tnfrsf1b,Trp73,Trpc6,Ucn,Uncx4.1,Utf1,Vax1,Vdr,Vgll2,Vipr1,Vsx1,Vwa2,Wnt1,Wnt10a,Wnt3a,Wnt4,Wnt9b,Xtrp3s1,Zfp536 GENE_SYMBOLS RALYL,,FAM89A,TDRP,PRXL2B,SYNE3,JHY,PLK5,,TMEM91,SNHG11,VAT1L,FBLL1,C6orf132,ABCG1,ADRA2C,ALDH1A2,ALK,ALX3,AMIGO2,SOWAHB,ATP12A,ATP2B2,B3GNT7,B4GALNT2,LRRC26,MAP3K21,TMEM150C,FAM167A,ADGRB1,BCL11A,BHLHE23,BMP4,BMP6,BNC1,BNC2,C1QL1,C1QL2,C1QTNF4,FAM163B,PPM1N,CABP7,CACNA2D2,CADM3,CALCR,CA10,CA7,ALX1,CARTPT,CBLN4,CCKBR,CDH1,CDH8,CDX2,CELSR1,CHAT,CHRNA4,CLDN7,CLSTN2,CNNM1,CNTN2,COBL,COL13A1,COL14A1,COL15A1,COLEC12,CPLX1,CPNE5,CPZ,CRB3,CRHR1,CRTAC1,CRYBA2,CXCL14,CYP26A1,CYP2S1,RBFOX3,STBD1,C12orf56,DACT2,DBX1,DEGS2,DLGAP2,DLX3,DMBX1,DMRT1,DMRT2,DMRT3,DOCK8,DPP10,DRD2,DSCAML1,CCDC92B,ECEL1,S1PR5,EIF4E3,EMX1,EPHA8,EVX1,EVX2,FEV,FEZF2,FGF14,FGF3,FGF4,FIBCD1,FLT3,FOXB2,FOXD3,FOXE3,FOXG1,FOXL1,FOXN4,FSTL4,GABRA5,GABRG3,GALNT13,GALR3,RAP1GAP2,GATA5,GFI1,GHSR,GJD2,GJB2,ANKRD63,,SHISA6,AJM1,FFAR4,GPR27,GPR37,GRIK3,GRIN1,GRIN2B,GRM7,GSX1,GSX2,HCK,HCN1,HCN2,HCRTR1,HECW1,HES2,HOXA11,HOXA13,HOXA9,HOXB1,HOXB2,HOXB3,HOXB4,HOXB5,HOXB7,HOXB8,HOXB9,HOXC10,HOXC13,HOXC6,HOXC8,HOXC9,HOXD10,HOXD11,HOXD9,HPCAL4,HR,HRH3,HS3ST6,HTR1A,HTR7,IGF2,IGF2BP1,IGFBPL1,IGSF21,IHH,IKZF1,IKZF3,IL11,IQSEC3,IRF5,ISL1,JAG2,JPH3,KCNA7,KCNH1,KCNK3,KCNK6,KCNQ1,KCNQ2,KCNS2,KCNS3,KCTD8,FAM43B,LAD1,LBX1,SKOR1,LEMD1,LHX5,LHX8,LIN28A,LIPG,LLGL2,LMX1A,LRAT,LRFN5,LSR,LTBP2,LY6H,MAL,MAL2,MAST1,MESP1,MIXL1,MPPED1,MSC,PHF24,NEFH,NELL1,NEUROD2,NEUROG3,NFATC2,NKX2-3,NKX6-1,NLRP6,NPAS1,NPAS2,NPR3,NPTXR,NXPH2,ONECUT3,OPRD1,OTOP1,OTP,OVOL1,OVOL2,SRCIN1,PAPPA,PAX1,PAX3,PAX7,PDGFB,PDX1,PENK,PGBD5,PGR,PHLDA2,PITPNM3,PITX1,PLXDC1,POU2F3,POU4F2,POU4F3,PPP2R2C,PRDM16,PRKCZ,PROK2,PROKR2,PRPH,PTF1A,PTH1R,PTPRN,PTPRT,PYY,RAB11FIP1,RAB11FIP4,RAB37,RASGEF1C,RIPK4,RPRML,RSPO1,RTN4R,RXRG,RYR2,SALL4,SCN4B,SCN5A,SCNN1G,SCRT1,SCUBE1,SERINC2,SFRP1,SFRP5,SGPP2,SIGIRR,SIM1,SIM2,SIX6,SKAP1,SLC12A5,SLC17A6,SLC22A3,SLC30A3,SLC38A4,SLC6A17,SLC6A3,SLC6A5,SLC7A14,SLC9A2,SLCO4C1,SLIT2,SNAI3,SORCS3,SOX18,SP8,SPINT1,SPTBN2,ST8SIA3,ST8SIA6,STAC2,STMN2,SULT4A1,SYT12,SYT2,TBXT,TBX21,TBX3,TCERG1L,TCF15,TFAP2B,TFAP2C,TFAP2D,NKX2-1,TLX1,TLX3,TMEM130,TMEM132E,TMEM151A,TMEM163,EVA1A,NALF2,TNFRSF11A,TNFRSF1B,TP73,TRPC6,UCN,UNCX,UTF1,VAX1,VDR,VGLL2,VIPR1,VSX1,VWA2,WNT1,WNT10A,WNT3A,WNT4,WNT9B,SLC6A20,ZNF536 FOUNDER_NAMES