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hESC exp1 hESC exp2 hESC exp3 hESC exp4hESC exp5hESC exp6 hESC exp7 hESC exp8 hESC exp9 ACTA1 CDC25A POU5F1 LUM ARID1B BRIX1 ORC1 POU5F1 CHEK2 ACTC1 CYP26A1 TDGF1 COL3A1 ARID5B CD9 PAK1 SOX2 CKS1B ACTN3 DNMT3A DPPA4 COL1A1 BHLHE40 COMMD3 IGF2 NANOG CCNB1 ADD2 DTYMK LIN28A IGFBP3 BTF3 CRABP2 C14orf156 HESX1 PODXL PARP1 EPHA1 NANOG ACTA2 CCDC6 DIAPH2 PHC1 ZFP42 TDGF1 ALPL ETV4 DNMT3B P4HA2 CDX2 DNMT3B SPARC ZSCAN10 TMSB15A AMD1 GPR19 TERF1 SPARC CEBPZ LEFTY2 NTHL1 TGIF1 PFN1 BIRC5 LPAR4 SEMA6A COL1A2 CNOT3 EDNRB RUVBL1 DNMT3A CFL1 ATP1A2 HELLS M6PR KRT18 COMMD3 FGF4 TTC3 DNMT3B DNMT3B BMPR1A MYBL2 SNRPN DCN CTCF FGF5 IGFBP3 LIN28A PCNA BUB1 ORC1 L1TD1 BMP4 CUX1 FOXD3 FAM89B NPM1 TERF1 BUB1B ORC2 LEFTY1 COL5A1 DBP GABRB3 PPAT FAS UTP18 C1QBP POU5F1 GAL COL2A1 DEK GAL ARHGDIB TDGF1 GDF3 CASP3 PWP2 SEPHS1 RHOBTB3 DLX1 GATA6 POLG2 GDF3 VCP CBS RBM4 GABRB3 NDRG1 E2F1 GBX2 TRIM37 FLJ21837 GJA1 CCNA2 TDGF1 SOX2 COL6A3 E2F2 GDF3 RNF138 DPPA4 CLDN6 CCNB1 ZIC3 LECT1 CST3 E2F3 GRB7 MTHFD1 HMGA1 NPM1 CDK1 HESX1 ANGEL2 KRT8 E2F4 IFITM2 TERF2IP ERH NCL CDC6 SLC5A6 BUB1 CD47 EBF1 IL6ST TDP1 CKS1B FAS CDC20 CLDN6 PSIP1 HAND1 EBF2 IGF2BP2 JARID2 CHEK2 SFRP1 CDC25A RRP9 IDO1 IGF2 EBF3 KIT ARL6IP5 CLDN6 FZD7 CTSC GDF3 HELLS CXCL14 EBF4 LEFTY1 LAS1L GJA1 Pou5f1 CHEK1 GJC1 GPC4 COL11A1 EOMES LIFR CEBPD ERH CRABP1 CHEK2 ITGB1BP3 IGFBP7 ERH LIN28A CTSB SOX2 CRABP2 WSCD1 CYP26A1 IL6ST Esrrb Nanog SEPHS1 LIN28A CRMP1 NCAPH MCM5 COL5A2 ESX1l NODAL DFNA5 HMGA1 CSE1L PRKD3 MTHFD1 KRT7 ETS1 NOG LUM ZFP42 CXADR GOLGA7 PPAT KRT19 ETS2 NR5A2 LCK CYP26A1 L1TD1 SLC16A1 BMP1 FOXA1 NR6A1 PPIC COCH ERCC6L NASP CDKN1A FOXO1 NFYC LOXL1 DHFR VRTN DLGAP5 FOXD3 NUMB CST3 DIAPH2 MCM10 UGP2 FUBP1 PODXL PARP2 DLG3 TXLNG MSH2 G3BP2 POU5F1 ESF1 DNA2 PRDM14 ZIC3 GATA1 PTEN GDF3 DNMT3A AEN PIM2 GATA2 REST LAMB2 DNMT3B DBNDD1 PLA2G16 GATA3 SEMA3A DCTN3 DSG2 DSCC1 ALPL GATA4 SFRP2 ANAPC1 ECT2 LIN28A AASS GATA5 SOX2 CSE1L SLC29A1 EPHX3 MGST1 GATA6 TDGF1 MCM3 EPHA1 NANOG GDF3 Gli1 TERT TERF1 EPRS HSPA4 Gli2 TFCP2L1 CCT2 ERBB2 PHF17 Gli3 UTF1 MEIS2 ETV1 UNG GSC Xist RFC3 ETV4 USP9X HAND1 ZFP42 POLE2 FABP5 CEBPZ HESX1 ORC2 FEN1 CRMP1 HHEX PPP3CC GPC4 BMPR1A HLX TRMT1 FGF2 ORC1 HMG20A MYST2 FGF13 HMGA1 GART FGFR1 HMGB3 LRRC20 FKBP5 HOPX NUP155 FOXO1 HNF1A DNAJB2 GABRA5 HOXA9 NR2F2 GABRB3 HOXB1 PHC2 GAD1 IFI16 COL5A2 GART ILF3 NUP107 GJA1 IRX1 CEBPZ GLDC IRX2 NCAPH GPM6B IRX3 SNRPB GPR19 IRX4 CHCHD3 MSH6 IRX5 DNAJC1 HAS3 IRX6 EHD1 HELLS JARID2 CRLF3 HMGB3 JUN C21orf59 HMGA1 KLF1 COL5A1 HMMR KLF2 GAS1 HNRNPAB Klf4 PON2 HSPA4 KLF5 PRMT3 HSPA8 LBX1 DHX15 HSPD1 Lef1 HSD17B4 ILF3 LEFTY1 PIM2 IDO1 LHX5 INPP1 ITPR3 LIN28A MAGED1 JARID2 MAF PRIM1 KAL1 MAZ DYNLT1 KCNS3 MED12 CRTC3 KIF5C MEIS1 WDR12 KLKB1 MEIS2 SIRT1 KPNA2 MLLT10 PARP1 KRT8 MRS2 USP39 LCK MSC COL3A1 LGALS8 MTA3 ANKHD1 EPCAM MTF2 EEF1E1 M6PR MYB YPEL5 MAN2A1 MYC RNF44 MARS MYCN SLC29A1 MAT2A MYF5 PITPNC1 MCM2 MYST2 PARVA MCM3 MYST3 DCPS MCM4 NACC1 PTCD3 MCM5 NANOG RAB22A MCM6 NEUROD1 EFNA1 MCM7 Neurog1 C9orf82 MFGE8 NFATc1 AGPAT5 MGST1 NFATc2 TSPAN3 MICB NFATc3 BLM MRE11A NFATc4 CLN5 MSH2 NFE2L1 PSIP1 NUDT1 NFE2L3 XPO1 MTHFD1 NFKB1 EDN1 NASP NFKB2 ORC3 NFYB NFYB DEK NODAL NKX2-5 MFAP5 NPM1 NPM1 NASP NTHL1 NR2F1 FRAT2 NTS OLIG1 VRK1 OAZ2 OLIG2 ADSL ORC1 OLIG3 RHOC PAK1 ONECUT1 S100A10 PCDH1 Osr2 PUS7 PDCD2 Otx2 NUP93 PDK1 PAX2 KIFAP3 PFAS PAX3 EFTUD1 PIK3CB PAX5 PLXNB2 PLCB3 PAX6 SLIT2 PMAIP1 PAX8 ACTA2 EXOSC9 POLR3G COL4A2 PNN POU2F1 PAICS PODXL POU2F2 DNMT3B POLE2 POU3F2 GUCY1A3 POU5F1 POU5F1 IVD PPM1B PRDM14 NLE1 PPP2R1B PSIP1 NUDT1 PPP2R2B REST POU5F1 PRIM1 RFX1 MCM6 PRIM2 SALL1 HSPE1 PRKX SALL2 CNOT1 PRPS1 SALL4 STX5 PTPN2 SKIL ELF4 PTPRZ1 SMAD1 ST6GAL1 RAB3B SMAD2 HMBS RARRES2 SMAD3 BUB1 RBBP8 SMAD4 POLR3E RFC3 SNAI1 TTC19 RFC4 SOX2 BTG3 ABCE1 Sp1 LEFTY1 ROBO1 SP3 TEX2 RPS24 SP5 DAP RRM2 SP8 BUB1B SALL2 SPZ1 GABARAP SALL1 SREBP1 VPS24 SCNN1A SREBP2 TMED3 SFRP1 SRF TRAP1 SFRP2 SRY NOL11 SRSF1 STAT1 LRP10 SRSF7 STAT2 MYBL2 ST6GAL1 STAT3 MRPS34 SLC6A8 STAT4 FN1 SLC16A1 TAF12 CD151 SMS TAL1 CAST SNRPA TBL1XR1 BAMBI SNRPN TBX3 ACAD8 SORL1 TBX5 ENDOD1 SOX2 TCF3 DSTN SSB TCF4 PRMT2 TDGF1 TEAD4 GSN TEAD4 TELO2 RELA TERF1 Terf1 CPSF4 TFAM TERT FKBP4 TIA1 TFAM LIN28A TMPO TFAP2A MCM5 TNNT1 TGIF1 TNFAIP3 UGP2 TGIF2 BCAR3 UNG THAP11 WDR45 VSNL1 TLE3 CHST4 ZIC2 TLX2 ARL2BP ZIC3 TP53 BACE1 ZNF195 TRIM28 AXL LRP8 TSC22D1 SKIV2L2 FZD5 TTF1 PLAT DEK TwIST1 GATA3 FXR1 UTF1 NFYB USP9X VDR TAF4 FZD7 WDHD1 SPSB1 UTF1 ZEB1 HJURP IFITM1 ZEB2 ADAMTS1 TMEFF1 ZFHX3 FBXO28 RUVBL1 ZFP161 EIF3B PPAP2A ZFP36L1 TCF25 USO1 ZFP42 NARG2 ADAM23 Zfx HMGA1 TRIM24 ZIC1 ZWILCH HESX1 ZIC2 RFC4 PROM1 ZIC3 CENPM FUBP1 WT1 KLHL20 DDX18 MYBL2 COL4A1 MAP7 ETV1 NUP54 CLDN6 ETV4 IDH2 SYNGR3 MYBL1 MSH6 BUB3 CECR5 DDX21 SF3B3 DCLK1 CHEK2 AURKB SEMA4D NOLC1 MORC4 PTTG1 DCLK1 MED14 PLK4 CER1 DYSF HOMER1 DYSF C1orf38 RAD51AP1 GDF3 HSPA14 NFE2L3 SMC6 DLGAP5 DAB2 G3BP2 TBRG4 RABGAP1L ANXA4 SRA1 ELOVL1 CHAF1A GNL3 DNAJB6 UPF3B AP1M2 L2HGDH G3BP1 STARD7 GPR64 HIP1 CEBPZ COL1A2 AASS ANXA1 PRMT3 SUPT16H ZNF267 DIAPH2 TRIM22 LRPPRC NPM3 NUP88 TUBB2C COPA LYPLA1 GLDC OLFM1 MTF2 MAD2L2 RANBP1 NOP56 CCDC53 PAICS GNAS POLR3G RMND5B RAD51AP1 GPR19 LEFTY1 MLLT11 IGF2BP3 GAS6 IGF2BP2 ECD MTHFD2 C17orf63 NMU CD47 KIF2C RABGAP1L PIM2 PMPCA NUDT21 HEATR1 LECT1 MAPKAPK5 DIDO1 MAPKAPK5 MYST2 SART3 PLA2G16 FCHO1 PSIP1 NUP160 WDHD1 ENOPH1 CHEK2 VSNL1 GPR176 EXO1 OIP5 EXOSC5 RRAS2 SMARCA2 MTF2 POLR2D SEPHS1 MMS19 RAP1GAP2 MPP6 TTLL12 ZNF185 PASK TMCO1 MDN1 HOXB2 COBL KIAA0922 BOP1 HMMR NCAPH CCT5 FRAT2 SDC4 SIRT1 TREX2 CBX5 TREX2 TNPO3 NUP85 PRKD3 C1orf38 KIF4A PLK2 RAD54B UNG NOL11 ZNF281 SFRS18 EMP2 LRIG1 MCM4 CNTNAP2 CSTF1 AUTS2 KPTN SERBP1 MPHOSPH6 PITPNC1 PPM1G GNL3 ANXA11 FOXD3 MBD2 ITGB1BP3 GGNBP2 NDUFAF4 E2F3 CYP2S1 DAZAP2 PYCR2 GOLGA3 RRP15 NCAPG2 GMNN LOXL2 GAL AASS FAM108B1 EFEMP2 PIPOX MRPL11 ZNF589 DLGAP5 RNF138 KCNK5 NOP16 PPM1B LARP7 CCNA2 ESF1 RMI1 AZIN1 KDM1A LSR BMS1 GINS2 SNAI2 GPRC5B TAPBP CECR1 ETHE1 BRWD1 SF3A3 MIS18A PIK3R4 FAM64A H2AFY PUS7 TPM2 EPB41L4B S100A13 L1TD1 DBC1 ERCC6L SYNGR3 ESRP1 ATOX1 NCAPG2 GMNN ZNF770 USP9X PAK1IP1 TRIP13 C12orf48 PUS1 FANCL PALLD DPPA4 WDHD1 VRTN RAB32 NUDT15 ZMYM1 BRIX1 LMCD1 MIS18BP1 PPP1CC LGR4 MUTYH MCM10 ZBTB3 PRPF40A BMP5 TMEM48 ADCY6 C12orf11 C16orf59 CCAR1 KRT10 WDR12 SGCE RCC2 MRPS17 KLHL7 HMHA1 CHST7 TSEN34 EXOSC5 SERBP1 NUP107 TMEM48 SALL4 MIOS SLC39A10 GPR124 MRS2 SLC10A3 SPC25 SS18L2 NLN BRP44L NLGN4X UBE2J1 MTA3 CER1 ZNF398 BRIX1 SEMA6A C10orf137 LRRN1 CDC20 CACHD1 PPT1 FAM60A NHP2L1 PRDM14 PPIH NOC3L CDT1 AEN SEC31A SLC13A3 MTIF2 CAPRIN2 NHP2L1 DBNDD1 TUBA1A CAMKV XRCC5 NUP37 LIG3 ELOVL6 PLD3 DSCC1 TWF1 GNPTAB NCOA6 AKIRIN1 MFSD1 NARG2 NFE2L3 LIN28A FASTKD1 NANOG MYL12A PHF17 MYL12A NAA15 CCDC92 MYO19 SET PUS1 H2AFZ TMEM177 PAK1IP1 SLC38A1 CKAP4 TMX1 TMEM9B WBSCR16 SNRPA CDT1 C16orf7 SPRY4 MMP2 TCF7L1 IDH1 BCL2L12 NUP153 USP44 STAU2 GINS4 CAPN2 HPS3 PCCB MAK16 TGFBI SLC7A3 PTTG1IP ZSCAN10 NUDC ANGEL2 NOC3L KIFC2 PEA15 C20orf72 PLK1 DMKN PLK1 EGLN3 G3BP2 CDCA5 BRP44 MAL2 CASC3 FAM46B NAE1 SCGB3A2 UGP2 GYLTL1B TRIM28 LOC157627 RAN C8orf42 SORL1 C11orf82 IFNGR2 ARL5B THOC1 TUBB2B SERINC1 CKMT1A MRPL16 LOC91431 GADD45A CD24 IL10RB CCT4 PCDH7 CCT7 LIMA1 MCM2 KLF6 ASNA1 CDC42EP1 PCNA LAMB1 BIRC5 LBH EPB41L2 IFI30 ZMYM4 C13orf23 EXT1 GATA6 ACVR2B WDR13 PTMA AURKB CALU LEPROT CPE BIRC2 RRS1 USO1 RPS6KA4 ZNF212 ARF4 GLB1 NOP16 TARS2 HOPX AQR DUSP1 S100A11 ATP6AP1 CUTC RAB31 THUMPD1 TGIF1 TNFRSF1A SMARCD3 APEH NSUN5 HAND1 EXOSC8 SAV1 MCM10 MYL9 HOMER1 DTL SUPV3L1 STIP1 C12orf11 ABCC1 NAMPT CLPX NGDN GNL2 NUP37 SMARCC1 CTCF AKT1 IGFBP7 DDX46 EFNB2 MRPL3 DVL3 THBS3 CCT8 MCM7 FOXJ2 DDX18 NDEL1 ANXA2 AGTPBP1 DHRS11 PAM16 SLTM CORT FSTL3 HBEGF CHST7 HHAT GALC KIF2A PRSS23 CDC123 DPH2 COPB1 COL6A3 CREB3 ARPC2 BRD7 LRIG1 MRPS2 ELF1 SSR2 PGRMC2 GHR GUK1 TDGF1 GCSH MAGED2 FAM60A ILK LEF1 CRMP1 HSPA2 DNAJB9 C8orf41 PRNP BCCIP KIAA0020 PHB PLS1 PEX11B C1QBP ZMIZ1 PIAS2 PPP1R15A TFB1M PASK ADAM9 DUT GCLC RRP12 HOXB6 TARDBP KPNA2 MAN1A1 PTS CYC1 COLEC12 EMP3 LGALS3 COL4A3BP BMPR1A PSMD1 MRPL42 FOSL2 MAP7 NDC80 SMC3 SMC2 SSB NUDT21 NIF3L1 KDELR2 NPM3 NOP56 KRT19 SEPP1 PNO1 CHEK1 GABARAPL2 CDV3 SUMO1 CDK11B KLHL9 FEN1 AKTIP BOP1 SCHIP1 DCTN2 COL2A1 TNPO3 MSH2 CDA SCNN1A CLSTN2 ZMYND8 SH3GLB1 CCT3 DUSP3 DSP DLK1 PHF17 C2orf47 WDR43 CXADR PLA2G16 PLOD3 ZIC3 UBE2E3 KHDRBS1 EVL NAB1 SNX3 KIAA0947 GOLPH3L XPA ADAR NLK TTK POLR3K RNMT FAM64A ZFHX3 CAV2 IPO4 WRN ME2 NCOA4 ABCB7 CDYL PWP2 ST3GAL5 ALOX5AP TUFT1 CKMT1B ABR DSC3 PMM1 PTBP2 DDT SNURF CCND3 ZC3H14 GSPT2 FBN2 CKS1B ARL8B SH3BGRL3 NNMT HERPUD1 WIPF1 CTBS AK4 DNAJA3 RPS6KA1 UBE2G2 PRAF2 ATP6V1F LSM3 WLS CAD ATG9A TAX1BP3 TAX1BP3 KLK6 NHP2 PELI1 DDX39A NDUFAF4 P4HA2 MYST3 FBN1 HSP90AB1 CADM1 LIMS2 CBS JOSD1 CTBP2 KLHL22 ABCF1 CTBP2 MAP3K4 KCNMA1 NSMCE4A TNFRSF8 SELRC1 JUND CXCR7 ACADVL IDE RAB1A VPS26A MKRN2 TSPO USP47 MRPL34 UTP6 KCTD12 PIPOX TNNT2 GPC3 SNRPC COX7C PSME4 COL16A1 GLMN FUS FABP5 ASAH1 CMTM6 RAB2A CDKN1A PDHA1 PTPN2 KIF22 CDC7 ARMCX3 RPRD1A DDX41 GTF3C1 KIF4A PMF1 TGFB1I1 RNASE4 PIGH RNASE4 WEE1 BAG3 TRIM16 RRP9 MTX2 ATP6V0A2 NRIP1 PMP22 ZFP36 ZWINT RIOK3 IMP3 PTPRZ1 TANK GCDH HSPA9 API5 TIMP4 IFI16 EFEMP1 ZFP36L1 CLTB MRPS30 SNRPA1 SRSF10 TPD52L1 SPOP C5 PRPS1 PRPS1 CBFB RRAS2 ARFGEF1 TUFM SIP1 ARAP3 SMPDL3A ISL1 C5orf15 TIMM10 RCN1 SRRM1 AHSA1 DNAJC11 SDCBP EIF3K FAH TNFAIP1 PRPF38B RARRES2 RTN4 ANXA8L2 THAP4 FANCL ANKMY2 THAP11 AURKA ACP6 TRAM1 GALNT2 LAMP2 CHAF1B CENPE SLC7A7 POLD1 RAD54L NMU HSPA4 OPA1 KIF20A TIMP1 PPAN HNRNPAB IL13RA1 TCP1 CHPF CSTF2 UTP18 BAD GIPC1 KRT18 XPO7 UBE2C FBLN1 DHODH SAE1 PSTPIP2 HIST1H2BE HIST1H2BK YBX2 RAP2C EPM2AIP1 VPS28 STK38 ACTR10 RBPJ USP10 PLSCR3 AIMP2 KCNQ2 IRF9 PHF10 COL11A1 ALG5 NCL MYBBP1A COL15A1 ARHGAP10 HSPB1 PES1 CUL7 NVL PIH1D1
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  • Supplementary Table S1. Upregulated Genes Differentially

    Supplementary Table S1. Upregulated Genes Differentially

    Supplementary Table S1. Upregulated genes differentially expressed in athletes (p < 0.05 and 1.3-fold change) Gene Symbol p Value Fold Change 221051_s_at NMRK2 0.01 2.38 236518_at CCDC183 0.00 2.05 218804_at ANO1 0.00 2.05 234675_x_at 0.01 2.02 207076_s_at ASS1 0.00 1.85 209135_at ASPH 0.02 1.81 228434_at BTNL9 0.03 1.81 229985_at BTNL9 0.01 1.79 215795_at MYH7B 0.01 1.78 217979_at TSPAN13 0.01 1.77 230992_at BTNL9 0.01 1.75 226884_at LRRN1 0.03 1.74 220039_s_at CDKAL1 0.01 1.73 236520_at 0.02 1.72 219895_at TMEM255A 0.04 1.72 201030_x_at LDHB 0.00 1.69 233824_at 0.00 1.69 232257_s_at 0.05 1.67 236359_at SCN4B 0.04 1.64 242868_at 0.00 1.63 1557286_at 0.01 1.63 202780_at OXCT1 0.01 1.63 1556542_a_at 0.04 1.63 209992_at PFKFB2 0.04 1.63 205247_at NOTCH4 0.01 1.62 1554182_at TRIM73///TRIM74 0.00 1.61 232892_at MIR1-1HG 0.02 1.61 204726_at CDH13 0.01 1.6 1561167_at 0.01 1.6 1565821_at 0.01 1.6 210169_at SEC14L5 0.01 1.6 236963_at 0.02 1.6 1552880_at SEC16B 0.02 1.6 235228_at CCDC85A 0.02 1.6 1568623_a_at SLC35E4 0.00 1.59 204844_at ENPEP 0.00 1.59 1552256_a_at SCARB1 0.02 1.59 1557283_a_at ZNF519 0.02 1.59 1557293_at LINC00969 0.03 1.59 231644_at 0.01 1.58 228115_at GAREM1 0.01 1.58 223687_s_at LY6K 0.02 1.58 231779_at IRAK2 0.03 1.58 243332_at LOC105379610 0.04 1.58 232118_at 0.01 1.57 203423_at RBP1 0.02 1.57 AMY1A///AMY1B///AMY1C///AMY2A///AMY2B// 208498_s_at 0.03 1.57 /AMYP1 237154_at LOC101930114 0.00 1.56 1559691_at 0.01 1.56 243481_at RHOJ 0.03 1.56 238834_at MYLK3 0.01 1.55 213438_at NFASC 0.02 1.55 242290_at TACC1 0.04 1.55 ANKRD20A1///ANKRD20A12P///ANKRD20A2///
  • A Preliminary Transcriptome Analysis Suggests a Transitory Effect of Vitamin D on Mitochondrial Function in Obese Young Finnish Subjects

    A Preliminary Transcriptome Analysis Suggests a Transitory Effect of Vitamin D on Mitochondrial Function in Obese Young Finnish Subjects

    ID: 18-0537 8 5 E Einarsdottir et al. Effect of vitamin D on gene 8:5 559–570 expression RESEARCH A preliminary transcriptome analysis suggests a transitory effect of vitamin D on mitochondrial function in obese young Finnish subjects Elisabet Einarsdottir1,2,3,†, Minna Pekkinen1,4, Kaarel Krjutškov2,5, Shintaro Katayama3, Juha Kere1,2,3,6, Outi Mäkitie1,4,7,8 and Heli Viljakainen1,9 1Folkhälsan Institute of Genetics, University of Helsinki, Helsinki, Finland 2Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland 3Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden 4Children’s Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland 5Competence Centre on Health Technologies, Tartu, Estonia 6School of Basic and Medical Biosciences, King’s College London, Guy’s Hospital, London, United Kingdom 7Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden 8Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden 9Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland Correspondence should be addressed to H Viljakainen: [email protected] †(E Einarsdottir is now at Department of Gene Technology, Science for Life Laboratory, KTH-Royal Institute of Technology, Solna, Sweden) Abstract Objective: The effect of vitamin D at the transcriptome level is poorly understood, Key Words and furthermore, it is unclear if it differs between obese and normal-weight subjects. f vitamin D The objective of the study was to explore the transcriptome effects of vitamin D f gene expression supplementation. f obesity Design and methods: We analysed peripheral blood gene expression using GlobinLock f transcriptome oligonucleotides followed by RNA sequencing in individuals participating in a 12-week f mitochondrial function randomised double-blinded placebo-controlled vitamin D intervention study.
  • RNA Epigenetics: Fine-Tuning Chromatin Plasticity and Transcriptional Regulation, and the Implications in Human Diseases

    RNA Epigenetics: Fine-Tuning Chromatin Plasticity and Transcriptional Regulation, and the Implications in Human Diseases

    G C A T T A C G G C A T genes Review RNA Epigenetics: Fine-Tuning Chromatin Plasticity and Transcriptional Regulation, and the Implications in Human Diseases Amber Willbanks, Shaun Wood and Jason X. Cheng * Department of Pathology, Hematopathology Section, University of Chicago, Chicago, IL 60637, USA; [email protected] (A.W.); [email protected] (S.W.) * Correspondence: [email protected] Abstract: Chromatin structure plays an essential role in eukaryotic gene expression and cell identity. Traditionally, DNA and histone modifications have been the focus of chromatin regulation; however, recent molecular and imaging studies have revealed an intimate connection between RNA epigenetics and chromatin structure. Accumulating evidence suggests that RNA serves as the interplay between chromatin and the transcription and splicing machineries within the cell. Additionally, epigenetic modifications of nascent RNAs fine-tune these interactions to regulate gene expression at the co- and post-transcriptional levels in normal cell development and human diseases. This review will provide an overview of recent advances in the emerging field of RNA epigenetics, specifically the role of RNA modifications and RNA modifying proteins in chromatin remodeling, transcription activation and RNA processing, as well as translational implications in human diseases. Keywords: 5’ cap (5’ cap); 7-methylguanosine (m7G); R-loops; N6-methyladenosine (m6A); RNA editing; A-to-I; C-to-U; 2’-O-methylation (Nm); 5-methylcytosine (m5C); NOL1/NOP2/sun domain Citation: Willbanks, A.; Wood, S.; (NSUN); MYC Cheng, J.X. RNA Epigenetics: Fine-Tuning Chromatin Plasticity and Transcriptional Regulation, and the Implications in Human Diseases. Genes 2021, 12, 627.
  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus

    A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus

    Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated.
  • 1 Supplementary Table S1. Primers Used for RT-Qpcr PROX1

    1 Supplementary Table S1. Primers Used for RT-Qpcr PROX1

    Supplementary Table S1. Primers used for RT-qPCR PROX1 (Prospero Homeobox 1) 5’ – CCAGCTCCAATATGCTGAAGACCTA – 3’ 5’ – CATCGTTGATGGCTTGACGTG – 3‘ MMP-1 (Matrix Metallopeptidase 1) 5' –CTGTCCCTGAACAGCCCAGTACTTA– 3' 5' –CTGGCCACAACTGCCAAATG– 3' FGF2 (Fibroblast Growth Factor 2) 5′ - GGCTTCTTCCTGCGCATCCA – 3′ 5′ – GCTCTTAGCAGACATTGGAAGA – 3′ MMP-3 (Matrix Metallopeptidase 3) GAAATGAGGTACGAGCTGGATACC– 3’ 5’ –ATGGCTGCATCGATTTTCCT– 3’ NUDT6 (Nudix Hydrolase 6) 5’ –GGCGAGCTGGACAGATTC– 3’ 5’ –GCAGCAGGGGCAATAAATCG– 3’ BAIAP2 (BAI1 Associated Protein 2) 5’ –AAGTCCACAGGCAGATCCAG– 3’ 5’ –GCCTTTGCTCCTTTGCTCAG– 3’ VEGFC (Vascular Endothelial Growth 5’ –GCCACGGCTTATGCAAGCAAAGAT– 3’ Factor C) 5’ –AGTTGAGGTTGGCCTGTTCTCTGT– 3’ ANGPT1 (Angiopoietin 1) 5’ –GAAGGGAACCGAGCCTATTC– 3’ 5’ –AGCATCAAACCACCATCCTC– 3’ KDR (Kinase Insert Domain Receptor) 5’ –AGGAGAGCGTGTCTTTGTGG– 3’ 5’ –GCCTGTCTTCAGTTCCCCTC– 3’ VEGFA (Vascular Endothelial Growth 5’ –CTTGCCTTGCTGCTCTACCT– 3’ Factor A) 5’ –AAGATGTCCACCAGGGTCTC– 3’ PLAT (Plasminogen Activator, Tissue 5’ –AGGAGAGCGTGTCTTTGTGG– 3’ Type) 5’ –GCCTGTCTTCAGTTCCCCTC– 3’ MDK (Midkine) 5’ –CCTGCAACTGGAAGAAGGAG– 3’ 5’ -- CTTTCCCTTCCCTTTCTTGG– 3’ ADAMTS9 (ADAM Metallopeptidase 5’ –ACGAAAAACCTGCCGTAATG– 3’ With Thrombospondin Type 1 Motif 9) 5’ –TCAGAGTCTCCATGCACCAG– 3’ TIMP3 (TIMP Metallopeptidase Inhibitor 5’ –CTGACAGGTCGCGTCTATGA– 3’ 3) 5’ –AGTCACAAAGCAAGGCAGGT– 3’ ACTB (Beta Actin) 5’ – GCCGAGGACTTTGATTGC – 3’ 5’– CTGTGTGGACTTGGGAGAG – 3’ 1 Figure S1. Efficient silencing of PROX1 in CGTH-W-1 and FTC-133 cells. Western blotting analysis shows a decrease in PROX1 protein level by targeting with siRNAs purchased from Santa Cruz (SC) and Sigma-Aldrich (SA) in both CGTH-W-1 and FTC-133 cell line. Beta-actin was used as a loading control of protein lysates. Figure S2. The tube formation assay. The silencing of PROX1 in CGTH-W-1 and FTC-133 cells enhances the angiogenesis in vitro of endothelial cells. HUVECs were cultured in 96-well plates coated with a semi-solid Matrigel.
  • 4-6 Weeks Old Female C57BL/6 Mice Obtained from Jackson Labs Were Used for Cell Isolation

    4-6 Weeks Old Female C57BL/6 Mice Obtained from Jackson Labs Were Used for Cell Isolation

    Methods Mice: 4-6 weeks old female C57BL/6 mice obtained from Jackson labs were used for cell isolation. Female Foxp3-IRES-GFP reporter mice (1), backcrossed to B6/C57 background for 10 generations, were used for the isolation of naïve CD4 and naïve CD8 cells for the RNAseq experiments. The mice were housed in pathogen-free animal facility in the La Jolla Institute for Allergy and Immunology and were used according to protocols approved by the Institutional Animal Care and use Committee. Preparation of cells: Subsets of thymocytes were isolated by cell sorting as previously described (2), after cell surface staining using CD4 (GK1.5), CD8 (53-6.7), CD3ε (145- 2C11), CD24 (M1/69) (all from Biolegend). DP cells: CD4+CD8 int/hi; CD4 SP cells: CD4CD3 hi, CD24 int/lo; CD8 SP cells: CD8 int/hi CD4 CD3 hi, CD24 int/lo (Fig S2). Peripheral subsets were isolated after pooling spleen and lymph nodes. T cells were enriched by negative isolation using Dynabeads (Dynabeads untouched mouse T cells, 11413D, Invitrogen). After surface staining for CD4 (GK1.5), CD8 (53-6.7), CD62L (MEL-14), CD25 (PC61) and CD44 (IM7), naïve CD4+CD62L hiCD25-CD44lo and naïve CD8+CD62L hiCD25-CD44lo were obtained by sorting (BD FACS Aria). Additionally, for the RNAseq experiments, CD4 and CD8 naïve cells were isolated by sorting T cells from the Foxp3- IRES-GFP mice: CD4+CD62LhiCD25–CD44lo GFP(FOXP3)– and CD8+CD62LhiCD25– CD44lo GFP(FOXP3)– (antibodies were from Biolegend). In some cases, naïve CD4 cells were cultured in vitro under Th1 or Th2 polarizing conditions (3, 4).
  • Supplemental Materials ZNF281 Enhances Cardiac Reprogramming

    Supplemental Materials ZNF281 Enhances Cardiac Reprogramming

    Supplemental Materials ZNF281 enhances cardiac reprogramming by modulating cardiac and inflammatory gene expression Huanyu Zhou, Maria Gabriela Morales, Hisayuki Hashimoto, Matthew E. Dickson, Kunhua Song, Wenduo Ye, Min S. Kim, Hanspeter Niederstrasser, Zhaoning Wang, Beibei Chen, Bruce A. Posner, Rhonda Bassel-Duby and Eric N. Olson Supplemental Table 1; related to Figure 1. Supplemental Table 2; related to Figure 1. Supplemental Table 3; related to the “quantitative mRNA measurement” in Materials and Methods section. Supplemental Table 4; related to the “ChIP-seq, gene ontology and pathway analysis” and “RNA-seq” and gene ontology analysis” in Materials and Methods section. Supplemental Figure S1; related to Figure 1. Supplemental Figure S2; related to Figure 2. Supplemental Figure S3; related to Figure 3. Supplemental Figure S4; related to Figure 4. Supplemental Figure S5; related to Figure 6. Supplemental Table S1. Genes included in human retroviral ORF cDNA library. Gene Gene Gene Gene Gene Gene Gene Gene Symbol Symbol Symbol Symbol Symbol Symbol Symbol Symbol AATF BMP8A CEBPE CTNNB1 ESR2 GDF3 HOXA5 IL17D ADIPOQ BRPF1 CEBPG CUX1 ESRRA GDF6 HOXA6 IL17F ADNP BRPF3 CERS1 CX3CL1 ETS1 GIN1 HOXA7 IL18 AEBP1 BUD31 CERS2 CXCL10 ETS2 GLIS3 HOXB1 IL19 AFF4 C17ORF77 CERS4 CXCL11 ETV3 GMEB1 HOXB13 IL1A AHR C1QTNF4 CFL2 CXCL12 ETV7 GPBP1 HOXB5 IL1B AIMP1 C21ORF66 CHIA CXCL13 FAM3B GPER HOXB6 IL1F3 ALS2CR8 CBFA2T2 CIR1 CXCL14 FAM3D GPI HOXB7 IL1F5 ALX1 CBFA2T3 CITED1 CXCL16 FASLG GREM1 HOXB9 IL1F6 ARGFX CBFB CITED2 CXCL3 FBLN1 GREM2 HOXC4 IL1F7