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210205_第4回彩の国女性研究者ネットワークシンポジウム
- 1. オンラインでの 研究者間コミュニケーション 210205 第4回 彩の国⼥性研究者 ネットワークシンポジウム @zoom 埼⽟⼤学 ⼤学院理⼯学研究科 ⽣命科学部⾨ 分⼦⽣物学領域 ⾼橋 朋⼦
- 3. DNA mRNA Protein 転写 翻訳 microRNA 分解 抑制 遺伝⼦発現
- 4. STAM2 SIX2 NFIB ZBTB14 C16orf74 MTDH PRSS42 C8orf37 CHIC1 OLFML3 CYP3A5 POPDC3 AQP4 PDE8A HSD11B1 TSPAN12 CDKN2A LPAR1 LCE3D BTF3L4 MARK1 TTYH2 FCHO2 BMP10 PRR20A C11orf30 GPR158 ARNTL2 NAGK ACER2 FZD4 CBX3 UBAP2L TFF1 PTPRT FAM19A1 AQP2 NEK3 SPRYD4 ASXL3 ZNF512B FBXW7 TAF11 BZW1 JMJD8 HBP1 SNURF KANK1 SKOR1 BZRAP1 NR5A2 KLRC3 ZNF728 STK4 GDF6 IGSF1 BEGAIN LMX1A XRN1 RAP1B DAND5 TFAP2C AL354808.2 CYP26B1 COLCA2 UNC80 BX255923.1 C1QL3 DIO3 BCL2L2 AKR1B1 NAALAD2 ZFP36L1 DERA CLVS1 AC006132.1 ZNF699 REPIN1 MCFD2 LAMTOR4 PHLDB3 RP11-113D6.10 TMEM98 RET TSN CEP76 GLCE HECTD2 RARB MED27 KRTAP19-2 DLGAP1 KLRB1 ZNF839 NCK2 DEFB129 NMRK1 SAMD12 RGL2 MMEL1 CAPN10 DCDC2 HSPA2 RNF135 HAND2 IL2RA FAM168B SWI5 CTSA TNKS2 PRR20E DUSP2 IQCJ-SCHIP1 VHL HN1 STAG2 LCOR SKP2 FAIM JPH1 TMEM245 CHCHD10 PADI4 TMEM234 TOB1 ELOVL4 TP53 DCAF6 COL5A2 XKR8 SLC1A2 TIMM8B ZFP69B SPARC MRPL13 OR5A1 PRKCE EREG EXD2 MAP3K3 NCAN PRRT3 RELA CDS1 ATXN2 GNG12 USP6NL CRLF3 RBBP9 CCND3 ISCA2 KIF23 BAIAP3 AKT3 CHP1 WEE1 PRR9 TECRL NUS1 WISP3 NCALD DOK6 ZFP14 SLC6A17 SELT TNFRSF9 UBE2L3 SNAI2 RP11-1C1.5 VASH2 COX6C RUNX2 COMMD3-BMI1 ZNF843 ARL4A ZBTB6 miR-605 EED DCDC2B ZNF259 AHR TRIM28 RSAD2 TOX2 DIP2A CHCHD4 ZNF292 PFKFB3 MDP1 EIF4G2 SRSF6 CLIC4 CPNE8 SERTAD3 CFL2 PPIH PRR20D E2F5 CYTH3 TECTA GPR137C TADA3 EYA1 ATP5J2-PTCD1 MOCS2 PROL1 RIMS4 KIAA1109 C1orf189 SLC25A18 KIAA1279 KIAA1024 ZBTB8B CD69 SFTA3 SLC52A3 KRT80 EIF4E2 MYH15 AHCYL1 SLC25A53 LEAP2 LPP MDH1 BDKRB2 LCMT2 CDK16 FAM196A RARG SP1 ERI3 ZKSCAN8 GGT7 ARSJ PRTFDC1 SYT3 FAM211B ATG9A ZNF784 FBXO21 HIF3A PHF19 ARMCX5 UHRF1BP1L EXOSC3 ZNF117 BLOC1S6 LCE1E ZNF470 SULT1B1 UNC79 MIOX FADS3 NRXN1 LUZP6 RAB8A PLG FAM43A TFAP2E COX7C SCN9A IL6R USP50 KLHL20 NAA40 CARD8 MYF5 HIST1H2BK BRMS1 SPCS1 BCAT1 JAKMIP3 PTS CREBL2 GJB5 DFNA5 RP4-758J18.2 CAMK4 UPRT EFHD1 F3 FAM188A S100A7A CHRM2 KIAA0232 BEAN1 GPR6 SOBP H2AFV SCAMP2 VGLL2 C6orf25 NEUROD1 SNN LRGUK PQLC2 TCF21 KDELC1 C8orf58 miR-25 ADAMTS17 NGF VEZT NFIA TPD52L3 FAM73A GNGT1 ASB6 PAX9 AC025278.1 ZNF468 RNF24 SUPT6H BBX TMEM200B KIAA1211L TMEM183A CNTFR SLCO3A1 BDNF DNAJC19 FAM57B DNAJC25-GNG10 PTPN4 TMEM154 GNAI3 CAPRIN2 EDA MPZ TMTC1 ADAMTS5 SLFN13 GABRA1 UBXN2A ZNF471 FLJ00418 DCUN1D5 ZNF30 JUNB PIM1 BET1L MED17 SYTL2 RHEBL1 ANKRD40 SCAMP1 UBE2I HIST2H2AA3 ACTR1B LHX8 GOLGA7 SLC2A5 PLAT ANKRD30BL IL1F10 C1orf43 GPCPD1 PHACTR3 miR-340 KLHL23 C10orf54 DLX5 BOD1L2 PPP4R1 TTK KLF1 SEMA4B miR-582 miR-1292 CENPQ RASGEF1B SLMO2 PDCD1LG2 C3orf83 ASPN TRAF3 miR-140 IL18BP ZFP36L2 PPP1R37 C5orf48 PEX11B ANP32E RNF39 TTC31 VTI1A ICOS PTAFR VAPB COL1A2 NR3C2 RGS4 PGC PDCL3 AK4 IAH1 AP003774.4 GBX1 CHD1 TBX5 PER2 UNC5C MAP3K7 RHO DBN1 miR-10b PKN2 GAREM DNAJC25 PCDHA11 AC011897.1 CDC37L1 CENPL TMEM74B C21orf90 YIPF4 LRRC8D GCG RNF34 GPRIN3 ZNF781 SKA2 EBAG9 SPATC1 DKFZP434E1119 ANKRD44 VASH1 NUP50 MYCT1 ATG5 RASSF2 AGAP3 GAN FAM49B ARL17B MKRN3 HOXA4 C8orf86 DNAJC2 HPX MBLAC1 GNG13 CASK CLLU1 PAPD5 VSNL1 LIN54 FBXO45 ZDHHC22 C17orf58 ANKRD1 GNG7 COX8C ERLIN2 CERS2 ARID4B OTX2 RANBP9 MARCH4 FBXO33 GLTSCR1 GRB2 REV3L PRKAB2 DCX DUSP5 UBTD2 BEND4 PTAR1 PTEN FOXP2 PTGFRN PCSK5 YOD1 CAMK2D XKR6 METAP1D KHDRBS3 BLZF1 SLC25A34 SH2D1A PRTG ZNF616 EFNB3 TBC1D16 FNBP1L MRPS35 MIP ATCAY VAT1L TMEM135 SLC2A14 MAP1LC3C KLHL3 ONECUT2 TLK1 RP11-817J15.3 PTPN3 TMEM38B FP15737 USP26 GTF3A PCNP TFEC S1PR1 FSD1L ZNF788 GPER1 EEF1A1 COPG1 SEC14L2 AL354993.1 ARPC5L SYCE3 PANX1 FAP VAMP7 C7orf10 INO80D TM2D2 YPEL2 ANKRA2 HGSNAT GPR3 ZBTB37 KRTAP4-3 RPS21 MAP3K2 ING5 PIH1D3 STRN3 HOXA5 TMEM62 SSPN PKP2 RP2 LSM11 LTBP4 CMTR2 OLA1 MNX1 ZNF800 CCNT2 SEL1L RBM24 KDM5A FLRT3 PIWIL2 C21orf91 SCGN RAB10 MOAP1 C1orf74 CPA4 NKX2-3 SH3BP5L LIPT2 GABBR1 ENHO DTX2 GCNT4 SUV420H2 CHTF18 MGAT1 C15orf43 GPD2 RSBN1 CCDC53 PREX1 LPHN1 UBE2F BAZ1B PRCC GJC1 GOLGA3 SLC44A5 TMCC1 ACVR2B GNG3 BTRC ABRA PPAP2A B4GALT6 KDSR AC008443.1 ANO3 CKS1B RBM7 NPEPPS SLC25A31 FBXO34 FUT9 ZNF780B AC008060.7 ESCO1 TNFAIP8 HPSE2 GLCCI1 TUBGCP6 GALNT3 PCTP ELMOD2 NMT2 CEP85L DESI2 CAMK2N2 HFE2 SNX16 AL078585.1 KRT15 RAP1A GNA12 TMEM204 H3F3A NME4 NRF1 EIF4E HOXB7 CCNI2 SLC16A1 CLCNKA NEIL1 RTN4 GDI1 HOXB13 HS3ST5 C8orf4 PFN2 SPRED2 ZNF207 OPCML SGIP1 EZH2 IPO9 DNAJB9 RP11-1212A22.4 CHIT1 SLC17A6 ARL5B CPEB2 CHST1 TRAF4 QARS EDNRB GPR37 PXT1 SGMS1 TRIB2 CINP C17orf78 C5orf34 ABCA7 RNF144B COMMD2 ZNF141 RBM23 EYA4 ESRRG FAM217B KLF3 GALNT1 NFE2L2 CAMKV NKD1 RNF139 CASR ACTN1 MKNK1 TMSB15B SIRT4 LRP5L CYB561D1 FAM83F PCDH10 TCERG1 SCRG1 HMBS CADM2 miR-181b/d PPT1 ANO8 IL36G SPTBN4 SLC25A25 ABCG1 SH3D19 NT5C3B PBRM1 LMO3 SH3GL3 KLHL28 INSR CEACAM8 miR-30a/b/e ZNF846 SZRD1 CEPT1 SPTBN1 CNBP RNH1 HMGA1 CCDC43 NCKAP1 HOXA9 MEOX2 MEX3B APPL2 NRG4 KMT2E LL22NC03-63E9.3 DDHD1 HGF SCN8A EPHA4 YWHAG KCNH7 CTDSPL FBXL20 HSPE1-MOB4 SERINC1 FOXN2 PTPN22 SGCZ ADRB1 KRTAP20-1 GNPTAB BTLA NAV1 MARS2 KDELR2 PPIC VSTM5 KCTD21 ELN IMP3 SERTAD2 ASMT ZNF732 miR-31 C21orf62 MIF4GD TAGAP ROCK1 H3F3B CYTH2 LDLRAD4 KLF11 MTCP1 FAM19A2 C2orf72 SMUG1 TMEM178B MT-ATP6 TGIF2 TNFSF14 PURA ATP6AP1L ZBTB34 CALM2 GH1 BEND3 PRRG1 ZIK1 QKI HMGN1 SPSB2 PIM3 FAM19A4 PSENEN CSMD1 PINK1 PTPRA CD9 DOLPP1 GPR45 C10orf126 RORA C17orf62 AIDA VPS54 CST9 C14orf144 ESYT3 CLYBL KISS1 CCNG2 CDKN1B ZNF528 CHODL RP1-170O19.20 ANO2 C2orf49 PITPNC1 BX088651.1 TES STK32C STAT3 DDX52 NACA MASTL MAP1LC3A CAV3 miR-106b DGKG STC1 C11orf44 MCOLN2 SH3BP5 IRG1 KLHL14 SPIN1 ZNF710 FAM20C ISG20L2 ARID3A RAB31 TMEM236 IGF2BP1 PIK3C2A COL3A1 RP11-10A14.4 HIF1AN RP11-463J10.2 AC016559.1 BECN1 TMEM182 CCDC180 AMIGO1 CBX6 H3F3C TNS3 ZC3H4 SMTNL2 FOXJ3 BRD2 PI4K2B RP11-162A12.2 PTK7 LHFP WIPI2 FAM189A2 C2orf42 C17orf97 TNFSF13B CCDC8 FAM200A CDON MANEA KLF6 KCNT2 ABCB5 RP11-366L20.2 TMEM86A SNX12 HECTD3 YWHAH APIP PPP2R5A PHACTR2 VIM SLC6A1 UGT2B15 LRRC17 AADACL3 CCDC78 RCN2 HSPD1 TMEM78 KIT HIST1H4L TJP2 PREX2 POTEM GINS2 LUC7L2 HOXA7 NXT2 CREBZF FCGR3A DHRS4L2 NDFIP1 NTNG1 FICD NFYA RIN2 FAM45A SCHIP1 C3orf58 ALPK3 MARCKS AEBP2 DKFZP779J2370 CPEB3 TPRA1 VANGL1 TEAD1 UQCR11 UFM1 PCOLCE2 YBX3 ZC3HAV1L PPP6R3 TPK1 IGDCC3 PRKAR2A ATAD2B TIMM9 TESK2 ERCC1 ZNF544 NRAS RFX4 ZNF525 GPR88 MMP19 ELOVL6 GABRA3 GPR107 CYTH1 ENY2 AMHR2 CHPF TRMT13 KIF1C CCDC89 IPPK DCTN5 RAB9B SPDL1 WNT3A FAM150A CEP290 PET117 POC1B-GALNT4 ZKSCAN1 DUSP16 STT3B HIST1H4I MAPK8 KLHL34 CYP4F22 RCAN1 AC073610.5 FBXO28 MRPL27 REEP3 TMEM25 GDE1 PDE7A CCDC86 CRISP3 VGLL3 PDIK1L NADK BMPR1A C1orf186 DNAH10OS SIVA1 PPP6R2 KIR3DX1 FAM160B1 HOXB8 KCNJ1 MAP7D1 RTN2 RP11-934B9.3 RASL11B TUSC1 NUP35 SP3 RRM1 FJX1 DTX4 AP3S1 GLIPR2 SMIM13 ABHD17C KIAA1875 UBE2Z YPEL3 KIAA1522 FHL2 DNAJC4 PSORS1C2 FAM150B COL19A1 TNFSF9 FAM118A SYPL2 FAM222B TIFAB TET2 DST UBE2K ADH4 CRISP1 SMURF2 DBNDD2 XKR7 ETF1 PTPRD PRKAA2 SSRP1 NAPB RORB KCNJ6 VDAC1 TSPYL2 TMEM14A ZNF423 SLC16A14 KCNN4 TSSK1B CDC42SE2 FBXL22 DNAJB4 MAP10 RNF128 PRKCD LRRIQ4 ZNF300 ZNF253 NUTF2 PDK4 PLN DEXI TMEM253 NPC1 HRK KCNK15 GCSAM ZBTB11 COMMD8 MTPN PTP4A1 ZNF257 IP6K2 NHLH2 PATE4 C1orf115 PLEKHA3 FAM86B2 RFC1 SMIM15 RCC2 TMEM215 UBE2H miR-196a NIPAL3 TMPRSS2 ZNF365 C3orf55 FOXG1 SFXN4 SLITRK3 CISD1 ZNF532 RHOC AFF4 DUSP1 WDR37 MRFAP1 miR-101 KCND1 HAND1 FAM227B MROH8 ARMC1 PIGG KLHDC8B MAP2K4 ZNF282 PBX3 MBOAT2 PMP22 USP44 ISL1 PI15 ZNF33A UCN2 REP15 ZNF490 CHL1 MACC1 ZNF676 TRIM44 CHMP4C EPHA8 WIPF2 TAF1 LIX1L SLC37A4 PSME3 DNAJA2 BCAP31 KIAA0226L RER1 TFCP2L1 RAB39A EMC4 RCVRN PLSCR4 HSPBAP1 PTBP2 SCD MICU3 ZNF667 NECAB1 SEC24C TPRXL ZC3H12C NAA50 VPS37D ANO4 miR-1226 MRVI1 ATG16L2 EDNRA BMI1 ARL9 TTLL7 CLDN4 MPEG1 EVI2B RIT2 MAP3K7CL SLC25A30 miR-3928 SAT1 ZFPM2 POTEG ATXN7L3B METAP1 SPINK9 ING1 NREP C15orf38 DHRS4 HNRNPA1 IRF1 CROT PVRL3 CDH8 FBXO48 SMARCA2 FOS SOX7 KCTD6 SLC25A28 SAMD1 MIA3 SLAMF8 METTL4 SLC25A32 SOD2 FAS ERGIC2 GSTA4 CDK8 PRELP ZKSCAN4 THRSP CREG1 MCMBP SMIM20 CACNG4 AIMP1 DDX11 GLG1 SLC2A13 ZNF208 KIAA0355 SETD5 CTD-2267D19.3 CASP2 RYBP FLRT2 miR-708 CUEDC2 RNF138 ITGB6 USP2 SOX5 CCND2 GPATCH2 TMEM100 KCNK4 SPRED1 AGGF1 GABRG1 C7orf41 ZC3H6 GALNT4 ZNF804B ATP8B1 CACFD1 CPSF2 ERP29 ENSG00000270466 miR-33b UCP3 UBN2 GPSM3 SCN2A JMY LYRM1 CCNE2 NDUFC1 PPFIA2 RAB27B LRRC37B LIMS3L ZNF513 C12orf79 C14orf178 ACTC1 NCS1 EHF PRKACB SYVN1 ADI1 ATP5E TMEM106C TSSK2 GPR34 VASP KCNK10 NUP188 ZNF385B GUCY1A3 B3GALNT1 PHLDA1 UBQLN4 HPCAL1 USH1C CREBRF AARS SPP2 MED19 GPR180 BRDT CRCT1 UGP2 MLIP PPP1R15B RNF183 TMEM169 TRIM71 RNF144A TET3 KRTAP19-7 HIAT1 C4orf22 SP140 ATPAF1 BTC MUC19 OSBPL10 RP11-644F5.10 ONECUT1 HS2ST1 RBM18 KCNA6 C3orf18 CRK RBP2 BTF3 RPL35 CACUL1 ALPP OMG CLEC17A CCNE1 LYG1 PRAC1 TNFRSF11B CCL28 ZNF136 miR-590 ST3GAL2 C9orf163 KIAA2026 TMEM229B EGR3 TRIM6-TRIM34 RP6-24A23.6 OTP SLC44A1 COL25A1 FAM162B NIPSNAP3B TNRC6A C11orf83 GALR1 TMEM167A NKX6-1 RNF4 DLX3 SMAD6 ARL14 SNX3 PANK2 C8orf33 CNST MARCKSL1 AKR1CL1 FZD2 FAM46B PRAMEF2 TLX2 AC004899.1 RRAGD EIF5A2 STAU2 PFKP SRGAP3 MRGBP TLK2 MYB TSPAN31 GRSF1 JOSD1 MPP1 ARL10 KLF2 FAM127A CDC25A LHFPL2 CDC7 SLC35D2 STK40 COL4A1 LIN28B MMP16 COL1A1 DES TBXA2R MYD88 SIRT6 HNRNPK RP11-67H2.1 miR-766 PLXDC2 METAP2 SNX18 EN2 SEPT3 SDC1 PCYT1B PDAP1 FAM102B FOXK1 SPI1 N4BP1 CCDC167 RBM6 CTC-349C3.1 ARL2 GJB2 AGO3 DCUN1D1 LRRIQ1 CTD-2140B24.4 GPR37L1 ISOC2 XXbac-BPG32J3.20 TMEM59 LL22NC03-75H12.2 GRIN2D TNFRSF13C PPP1R2 FHL5 LRP5 MIER3 SKAP1 PAFAH1B2 ZNRF1 PRPF31 NPLOC4 PRKRA ZNF765 BST1 NT5C1B SOX12 C6orf164 MED28 TOX3 Z98049.1 CDYL NSFL1C ANKRD10 HMGB3 ITPKA RP11-455G16.1 HNRNPA3 TBC1D13 FAM210A HS6ST2 NPNT C1orf63 PAK2 PIEZO1 CSNK1G2 MEMO1 LIN52 RIT1 PLEKHA1 GDPD5 EIF4G3 KIAA1432 RP11-676J12.7 MED8 NSF ZBTB5 LRIG3 PTPLAD1 SLC22A7 ARID3B NDRG3 miR-29c FAM169A EGLN3 AC124890.1 ANAPC11 PSAP TBCA ZFAND5 TRNP1 ARHGAP36 CELF2 SFXN2 CTDNEP1 FLJ20373 MGAT3 PLAGL1 CD1E JOSD2 NHLRC3 FAM133B GLT1D1 UBE2V1 KIAA1324 SIX6 SDHAF2 TNFRSF10C PNRC2 SCP2 ZNF397 NUDT18 METTL9 MARCH2 APPBP2 PROP1 ZNF385A MAGEB5 GNG10 FAM196B CDK2AP1 ATP8A1 C2orf88 EBLN2 TMEM170B GAS2L1 PIEZO2 C1QTNF3 PLEK2 AP000867.1 SELK PTPRG HABP4 PNO1 TMX1 ARHGAP29 ELF1 BSND ZNF224 EWSR1 CLEC4E PRX RGS17 SP5 ATG16L1 RP11-160N1.10 RBM25 SERP1 NR2F2 ATXN1 KPNA6 ABHD2 HTATIP2 PTCD1 GNAQ AL353791.1 IL6ST DUSP10 HARS2 DDX19A ZFYVE21 HAPLN3 PRSS22 LATS2 COL4A5 let-7a GXYLT1 SH3BGR KSR2 CRYBG3 KLF17 SPHAR KLHL18 HOXB6 TRIM2 LURAP1L KCNC3 ZNF367 RNF150 PHC1 RPRD1A miR-324 CHEK1 C17orf102 CACNA1I C6orf201 SMAD7 SLCO5A1 ZNF622 SCGB2A2 miR-16 DCTD SST ASAH2B APOL6 KRBOX4 CCZ1B CACNA1C TMEM129 ITGBL1 TMEM257 LRP3 CXCL5 GMNC GPR161 NSL1 SLC7A10 VAT1 FOXS1 UBE2V2 ATP5C1 KCNA5 HERPUD1 CSNK2A1 SLC9A3R2 BAI3 RDX CCL8 BTBD10 PSMD11 ADM C7orf55-LUC7L2 HSPA1B PMAIP1 UBE2E1 AP001579.1 miR-500a PPTC7 SPG7 FGD4 TSTD2 GCLC NKIRAS1 HMGN3 HTRA3 ST5 BCL2 IDO2 CAMKK2 RNF141 ZC4H2 SBDS G3BP2 ZNF506 APBB3 BCAT2 TPM1 GATM BMPER NASP GSX2 CD28 VGLL1 SMIM5 TMPRSS11F A2ML1 SPINK4 DERL2 METTL17 CTNNBIP1 SRSF1 TP53INP2 SSX2IP POU6F2 RAN USP46 SFRP2 G2E3 C20orf197 HELZ FAM9B GPR63 TRMT1L SPRYD3 FAM92A1 NEGR1 CCNG1 THAP1 ARF6 AC107021.1 ZNF256 TPRX1 SETD9 LETMD1 CPT1A GRPEL2 BIN1 ANKRD7 C10orf11 KIAA1161 RGS9BP E2F7 SHC4 NSG1 WDR82 HILPDA GJB7 NBEAL1 LUM TMEM14B MLF1 EPHA7 SAPCD1 SUMO2 LOR MBD2 LGR5 MBOAT7 CCDC6 MSRB3 SEC14L6 ANKRD52 ABCC8 ZDHHC21 ITPRIPL2 RRAGC SOCS5 PTHLH PPAP2B KBTBD8 ADD2 CDK6 TACO1 CDC20B RHPN2 GH2 TSPAN17 IDH1 DNPH1 ADAMTS8 PPCS LOXL2 SALL4 MAP4K5 IREB2 PGF HOMER1 LAMTOR3 FAM212B PC METTL10 RRP7A DDTL NCOA7 RNF165 C16orf52 RGP1 CECR6 CCDC113 PCDH19 ELOVL2 SERPIND1 PEX13 VSIG10 MTMR11 ZNF69 SETD3 DARS KRTAP4-4 C3orf72 NQO2 TMPRSS11BNL UBE2W PARK2 PLGRKT ZFP62 HGD STRBP SPINK6 PLEKHG5 GRIK2 GRAMD2 NFIX CATSPER2 TIA1 B3GAT1 LUC7L3 C7orf43 CTC-360G5.1 LCTL IL1RAPL2 ACADS RPA1 ICAM5 ZNF630 EPN3 HNRNPH3 SNAP91 PHF2 ATXN7L2 ZBTB26 C4orf26 ELAVL3 C1orf213 MRFAP1L1 CTH FAM163A MAPRE3 NOVA1 ERGIC1 FAM219B RHOA SULT4A1 EZH1 ADAM10 CACNB2 LAS1L RBFOX2 SCGB1D1 UCK1 ARRDC3 C10orf25 BMP2 MORC3 GPR174 STX3 SLC12A5 SS18L1 SMIM3 PXK SMIM17 CCDC88B RASA1 EFCAB5 SYNE2 CIAPIN1 POLR2K GREB1 GPX3 CHI3L2 DOCK11 LPPR5 APOLD1 NPAS3 LYPD3 ARF3 NCOR2 KRTAP1-3 DIXDC1 TXNL4A TMEM55B GTSF1 AXIN2 AL355390.1 DESI1 LY6E C9orf153 OCSTAMP RPL30 DERL1 ACSL6 ZFP30 SPATA2L SNX9 ANKRD23 CISD3 TM9SF3 SSU72 SUV39H1 C14orf132 RP11-497E19.2 C7orf25 TRIM34 ZPBP2 HPGD RPP25L CYP24A1 NLGN4X DUSP18 ANO6 LCK MRS2 IFNG SSR1 CTD-2330K9.3 PLA2G16 RXFP2 ZNF599 KIF13A KCNAB2 NGDN NOV LARP6 PPP3R1 CCDC178 TUBGCP4 RGMA AP2A2 MTMR2 BRMS1L GAB2 RAB1A PRIM2 RP11-650K20.3 ACSBG2 RBMS1 CEP41 KRTCAP3 CD226 RBM47 CCHCR1 AC010441.1 SNAPC1 SESTD1 HOXB1 CACYBP COL5A3 STX10 PAX5 REG3G LRR1 IL34 VPREB3 AC174470.1 MSL2 VWC2 BCL6 MAPK6 ABL2 KLF7 EOMES SHPK KLHL29 LAMB3 CHAC1 HAPLN1 RAD9A KDELR3 RSPO3 METTL21B NEK10 CDKL2 CSRNP3 miR-1304 SIM1 ZNF33B ST8SIA1 OSBPL3 C6orf195 UNCX RPP25 HIF1A SPAST PLLP KCNAB3 CASP9 STX2 TSHZ2 MTMR8 ELOVL5 SNX4 COPS2 PAPD4 RP11-382J12.1 C20orf202 ATF1 ZNF493 PPP2R3A GRIK1-AS2 TBPL1 TMEM139 TVP23B ERI2 FAM127B SLC4A4 PMM1 MRPL43 JAM3 AP5S1 CDKN1A AP1S1 MICAL1 CLIP4 SLC30A3 EMP2 CYBRD1 MCTS1 MORN4 GSTM5 VANGL2 C1orf200 MFSD7 TMEM229A IP6K3 KIAA1429 NEFM BOK PDE12 MYO1B TSPAN14 RNFT1 TMEM43 LYSMD1 TRUB2 SEPHS1 CCL27 MRPS17 TFRC AKAP4 SLC38A8 TTC39A WFDC13 NEDD4 TEF ITGA9 ALPL PSMF1 AP1G1 NR6A1 WNT2B CXCL10 CHMP2B FAM122A LYSMD3 TMEM55A TXNDC8 SNCG AC105020.1 SH3BGRL RAB30 AC018816.3 ZNF426 DTWD2 ZNF302 PTGER4 RASSF8 LSMEM1 DBNL GAS1 GGCT SH3BGRL3 TMEM45B ELAVL2 AIF1L CCL14 C9orf72 KCNIP3 C15orf56 GSKIP CSNK2B-LY6G5B-1181 HYPK DDX5 ZNF561 NOP9 MZT1 POTEE GPANK1 UBE2D1 CALM1 TAF1D EPC2 TPBGL AP3B2 COQ10B MYL9 ZFAND4 RP11-122A3.2 CAPN5 VLDLR UBXN10 CDH5 IRF9 MEIS2 SUB1 SUFU CBL KRTAP5-11 KIF2A CHST7 GEM RSPH4A CBLN4 TMEM218 DPH3 CLDN11 PGAP2 CDC34 IDE CYCS SNX20 FAM60A ARSK POU2AF1 SSH1 HTR1F ZNF233 CDCA7L SNRPN NR4A3 NANOS1 KLF13 HAS3 GON4L PBX1 DAZAP1 FRMD4B CLDN12 PRELID1 MAPK8IP2 AMELY AC068987.1 NF2 SLC9A8 CXCL13 DAOA NLN RAD54B RBBP7 CD2AP ZNF268 TVP23A SATB2 ZNF227 FDX1L SREK1 AKR1C4 TGFB1 RORC ACTR3C COA1 EFTUD2 RRAD MOSPD1 FAM3C LGI1 AMOTL2 CXCR5 CXADR RP11-204N11.1 RGS1 AGAP2-AS1 TMEM143 USE1 IGFBP3 GLTP TMEM174 PHF13 CD151 AC006372.1 FZD3 RAB3D TRIM3 C16orf87 BAD BAMBI CD274 MBNL1 CCL1 LYG2 PROK2 SFT2D3 REEP5 C1orf110 DACT1 PLEKHB2 ADH6 PAG1 TGIF1 BBOX1 ADRB2 RPL15 CDC42 TGFBR1 APBB2 COL2A1 NGB AMER1 AGTR2 APOM PDZD2 CALCB MYO9B TEX261 NAT1 WWC2 DKK3 SLC6A4 IGDCC4 TMEM260 FAM175B FIGN NRGN KIF5A P2RX4 miR-503 LDOC1 CCND1 EFEMP2 SLC9A6 NMUR2 CST7 HOXD1 C2orf76 CPNE2 ZNF530 ZNF23 PKD1L2 AC007405.2 LYRM5 PCYT2 ABCA1 ARMS2 PPP5C TMEM65 SYNGR3 GREM1 GCH1 RFX6 RABGAP1L MRPL2 SRSF7 LRRC55 CDIP1 NOG CCDC22 ZBTB25 WNT11 MAP4K3 ZNF133 LEPROT SENP6 TET1 CCNJ GCN1L1 PLSCR5 CD81 RPA3-AS1 UEVLD MAEA DEK TGFBR2 FCRLB SGK1 PKD2 SDC4 MFSD6 ZDHHC9 SLC10A4 GMFB NPAS4 SHOX TNFAIP1 FAM179B KLF4 RP11-701P16.2 RAB15 GLRA1 FBN1 LPGAT1 PCDH8 C7orf73 ZNF845 SEMA6D DTD1 CCDC69 SYDE2 TMEM70 ZNF195 OTOF HSPB8 PALM2 E2F6 DLG4 RAP2A NNAT SLITRK4 HCN1 TNFRSF1A WBP11 LRRC37A3 SEPT2 VOPP1 SMPD1 CTD-2616J11.4 CCDC19 KRT32 GUCY1A2 HOXA11 IFT27 ESM1 ZYG11B ZNF655 TPCN2 TMED5 C10orf76 PCDHB16 DEPTOR C19orf69 AC026202.1 CAP2 SMAD1 SYT13 FAM204A SRSF10 C3orf70 MTRR GABRB1 ZNF415 EPB41L2 COX17 FAM86B1 GYPE SNX6 ABCB9 C12orf76 HOXB2 POLR3D TCF19 HNF4G AOC3 ZNF711 PAXBP1 ANKRD13A FBXL5 INSIG2 BMP4 DYNC1LI2 WDFY1 TGFA VSX1 MAPK1 ZNF654 DYRK1A ZNF146 AC021218.2 ATG12 RNF38 DYNLT1 GOLT1A DUS2 DEFB126 DDX19B BTG2 MPZL3 C5orf51 KIAA1462 ADAMTS2 ODF3L2 TMED10 IFI44 SIKE1 FGF7 SAMSN1 GIPR TRIM26 TRIM8 KCTD16 RP11-192H23.4 SMARCD1 ZMYND11 CDKN2AIP RNF214 GATA6 NPY1R CCNYL1 ZNF488 VEGFA UQCR10 KCNJ2 ZNF474 HTR2A C5orf45 SNRPF KIAA0195 HORMAD1 C2CD5 GABPA RBAK TIMM17A NIPAL4 ITFG2 PHB2 KIAA0087 TBC1D22A C15orf37 LPAR4 SEC23A TNC MBTD1 RAB32 TUB FCGR2B PIP4K2A VSIG1 C11orf88 KCNS3 RNASE10 CCDC144NL IL4 GALC TGM1 C5orf47 ZNF385D AL009178.1 VWC2L PTGS2 PRAMEF13 UBE2D3 LRRC69 LIMA1 TIMM23 APBB1IP ARHGAP12 NDST1 COTL1 BTG3 FGF9 C1orf52 ZNF514 TTC1 AC079354.2 PHF7 TMF1 GPAT2 SDAD1 EPB41L4A-AS2 RP11-386G21.1 TARBP2 MAN2A1 CCSAP BACH1 OAS2 ADAMTS9 LELP1 LBH GNE CCDC70 PEX5 TNFAIP8L3 ZNF594 YWHAZ SULT6B1 JARID2 URGCP NIPBL IL1RAPL1 GPM6A RNF44 KPNA5 MYL1 SLC2A3 AC012215.1 MOB4 LINC00632 ZBTB16 CCL23 CDCA4 TCP10L2 CSH1 ARHGEF3 C10orf40 ZFAND6 GABRA4 ZNF286B KAT5 RNF115 GRIK5 UNC13A HADHB CAAP1 SCRT1 CXorf61 EVX2 RNF103 ACTR2 SOCS1 miR-218 C9orf135 TWF1 LMNB1 CRTAM KIAA0895 HEPN1 CTXN2 NT5C1B-RDH14 RSPO2 AIMP2 MAL MAP3K1 DUS4L TCF4 ADAMTS18 SOCS2 SLC35A2 TK2 E2F1 GPX8 CCDC151 MYT1L SSR3 TNPO1 RAB22A KCNK17 ABHD17B UCK2 GOPC RP3-422G23.4 HDDC2 USP28 MESP2 TMED7-TICAM2 UBXN4 H1FOO GEMIN7 HIPK3 COL9A1 CCL7 MIXL1 C1QTNF6 OMP AP000695.1 CCR1 ZNF813 PSMB11 ACN9 PVALB CCDC42B ORC4 MDGA2 DRAM1 APP CNNM4 HOXB3 ZFX SMAP1 HNRNPA1L2 DYRK1B ABCA13 PCDHAC2 TPD52 PAPPA LEPREL1 MAMSTR MYC DGKE C2orf69 DSG1 CTD-2228K2.5 N4BP2 ZFP82 C1QTNF9 NAA15 NDRG4 CD248 ANKAR NUP153 PAX2 ZBTB43 RAD23B KIAA1456 PRLHR ZDHHC20 GABARAPL2 RP11-861L17.3 STOX2 MALL KLF10 ALAS1 AGA AC069547.2 APLN SDCBP FLG2 B2M LARP4 DMRTA2 SLAIN1 SYCE1L ZNF98 SCN1A MSRB2 SQSTM1 PRDM12 UCMA SLC17A7 HOXB5 NUDT11 HAUS8 SPPL3 NLK ACYP1 CCDC179 MAPK13 PEF1 OAZ3 TNFAIP6 IMPG1 CNIH1 KRTAP10-11 MYCN RAB23 COL7A1 MDM4 KCNN3 COL11A1 ASPHD1 FLOT1 GGT6 SALL1 WDR5 IDS FAM58A YIPF3 CNOT7 KIAA0247 GLP2R NUP43 PIK3CA AS3MT ELAVL1 RNF186 CDSN PAM CBLN3 USP25 STATH ZNF697 OR2H1 AQP11 ACSM4 SLC33A1 ITSN1 GLRA3 RLF XKR4 ZNF266 TBC1D9B SMARCA5 SLC17A9 SLC5A10 LDHA SFXN1 miR-744 EIF4E3 AC104472.1 RCBTB1 PDXDC1 GNA13 CPEB1 RP11-180C1.1 TMEM181 CCR2 BCL2L11 FDX1 LARP7 UBE2L6 SGCE EXOC5 miR-345 ARG1 DIRC2 TMEM213 ATP5G3 METTL7B HPCAL4 PARD6B C15orf53 ZFP3 CRISPLD1 PRR20C ZNFX1 PLEKHG3 C10orf88 ENPP5 RNF7 STMN1 HSPA12A ZNF131 ZNF319 TOB2 SRPR RP11-1102P16.1 PDIA4 GRAMD3 ITGA11 COIL B3GALT2 COL21A1 FAM103A1 NUMB IFI30 METTL21A FAM53B PATE1 SLC8B1 ARHGEF2 CASP3 KIAA0513 ARIH1 miR-126 EPHA2 TXNL1 SOX1 GABRB2 MARCH9 KCTD20 SLC6A19 MICA ANKS1A GRAPL HMGA2 CETN2 C1orf21 RPL23 PTH TCP10 TCEAL3 RAB3IP FAM183B APOO ALG10B ZNF487 MDGA1 EGFLAM NEU1 CSMD2 ZNF281 CXorf58 SNTB2 SREK1IP1 HOXA1 ST8SIA5 SLC11A2 LIN28A CMKLR1 SEC61B B3GNT5 CDK20 FAM3D RAB11A FAM86C1 IAPP KRR1 ERG KCNA1 RANGRF PACRGL C5orf30 CXXC4 SAMD10 PRAMEF14 MAPRE1 RP11-93B14.6 NABP1 ZNF804A PRR20B RGMB MAFG C10orf107 ZBTB7A CCDC85C ZMAT3 LENG9 CASD1 PAPSS2 ALS2 NECAP1 SLN miR-378a CNEP1R1 miR-2278 GNG5 FNIP1 COL4A4 ARHGEF38 VPS26B TDG GPR132 DCBLD2 S1PR3 ZNF791 TMEM145 HOXC8 ZNF83 KIAA1430 FBXL2 ACTG1 SPRY3 ST6GAL2 LRRC8B AL441883.1 MOCS1 HOXA3 TP53INP1 ANLN UBE2E2 DGCR2 miR-636 CNOT6L AL161915.1 WNT7A AC024940.1 CD84 CPOX LRRC58 BHLHE40 DGKH ZNF283 TMEM51 TTC28 ROGDI SZT2 BEND6 AC002472.13 LRIG1 CYB5D1 PTPN13 PLCL2 KRTAP4-8 CAMK2N1 microRNAによる転写後遺伝⼦発現制御 ネットワーク ヒトの遺伝⼦ ヒトのmicroRNA 約20,000 約2,000 1つのmicroRNAは 複数の遺伝⼦を 同時に制御する 1つの遺伝⼦は 複数のmicroRNAに 同時に制御される ・ ・ microRNAと遺伝⼦は ネットワークを形成する ・ 特定のmicroRNAの発現変動は 遺伝⼦発現ネットワークを 異なる状態へ移⾏させる
- 6. ウイルス学若⼿研究集会2020（2020年12⽉@zoom） 〜オンライン若⼿の会〜 Small RNA-directed immunity Source Target RNA vs Target Function siRNA Exogenous viral RNA Exogenous viral RNA 1 vs 1 Cleavage of viral RNA microRNA Endogenous genome Endogenous gene Network Regulation of gene expression (adaptation to antiviral state) piRNA Endogenous viral element Exogenous viral RNA 1 vs 1 Cleavage of viral RNA ~ Small RNA駆動型免疫 ~ Antiviral mammalian immunity directed by microRNAs Saitama University Tomoko Takahashi 201218-19 Virus-Wakate meeting 2020 @Zoom @tomokotakahas
- 7. ENCODE3勉強会（2020年8⽉@zoom） 〜オンラインジャーナルクラブ〜 ARTICLE Regulation of RNA editing by RNA-binding proteins in human cells Giovanni Quinones-Valdez 1, Stephen S. Tran2, Hyun-Ik Jun3, Jae Hoon Bahn3, Ei-Wen Yang3, Lijun Zhan4, Anneke Brümmer3, Xintao Wei4, Eric L. Van Nostrand5,6, Gabriel A. Pratt5,6,7, Gene W. Yeo5,6,7, Brenton R. Graveley4 & Xinshu Xiao 1,2,3,8,9 Adenosine-to-inosine (A-to-I) editing, mediated by the ADAR enzymes, diversifies the transcriptome by altering RNA sequences. Recent studies reported global changes in RNA editing in disease and development. Such widespread editing variations necessitate an improved understanding of the regulatory mechanisms of RNA editing. Here, we study the roles of >200 RNA-binding proteins (RBPs) in mediating RNA editing in two human cell lines. Using RNA-sequencing and global protein-RNA binding data, we identify a number of RBPs as key regulators of A-to-I editing. These RBPs, such as TDP-43, DROSHA, NF45/90 and Ro60, mediate editing through various mechanisms including regulation of ADAR1 expression, interaction with ADAR1, and binding to Alu elements. We highlight that editing regulation by Ro60 is consistent with the global up-regulation of RNA editing in systemic lupus erythe- matosus. Additionally, most key editing regulators act in a cell type-specific manner. Toge- ther, our work provides insights for the regulatory mechanisms of RNA editing. https://doi.org/10.1038/s42003-018-0271-8 OPEN 1234567890():,; ARTICLE Regulation of RNA editing by RNA-binding proteins in human cells Giovanni Quinones-Valdez 1, Stephen S. Tran2, Hyun-Ik Jun3, Jae Hoon Bahn3, Ei-Wen Yang3, Lijun Zhan4, Anneke Brümmer3, Xintao Wei4, Eric L. Van Nostrand5,6, Gabriel A. Pratt5,6,7, Gene W. Yeo5,6,7, Brenton R. Graveley4 & Xinshu Xiao 1,2,3,8,9 Adenosine-to-inosine (A-to-I) editing, mediated by the ADAR enzymes, diversifies the transcriptome by altering RNA sequences. Recent studies reported global changes in RNA editing in disease and development. Such widespread editing variations necessitate an improved understanding of the regulatory mechanisms of RNA editing. Here, we study the roles of >200 RNA-binding proteins (RBPs) in mediating RNA editing in two human cell lines. Using RNA-sequencing and global protein-RNA binding data, we identify a number of RBPs as key regulators of A-to-I editing. These RBPs, such as TDP-43, DROSHA, NF45/90 and Ro60, mediate editing through various mechanisms including regulation of ADAR1 expression, interaction with ADAR1, and binding to Alu elements. We highlight that editing regulation by Ro60 is consistent with the global up-regulation of RNA editing in systemic lupus erythe- matosus. Additionally, most key editing regulators act in a cell type-specific manner. Toge- ther, our work provides insights for the regulatory mechanisms of RNA editing. https://doi.org/10.1038/s42003-018-0271-8 OPEN 1 Department of Bioengineering, University of California Los Angeles, Los Angeles, CA 90095, USA. 2 Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA 90095, USA. 3 Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA 90095, USA. 4 Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT 06030, USA. 5 Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA. 6 Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA. 7 Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA 92093, USA. 8 Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA. 9 Institute for Quantitative and Computational Biology, University of California Los Angeles, Los Angeles, CA 90095, USA. Correspondence and requests for materials should be addressed to X.X. (email: gxxiao@ucla.edu) COMMUNICATIONS BIOLOGY | (2019)2:19 | https://doi.org/10.1038/s42003-018-0271-8 | www.nature.com/commsbio 1 1234567890():,; of editing levels upon knockdown were obtained. Pairs of RBPs with less than 20 total shared differentially edited sites were not considered (thus with no links in the plot). Then, we obtained the number (t) of shared testable sites in the datasets of the two RBPs. The ratios n1/t and n2/t were then calculated, where n2/t was reported as -n2/t to represent the opposite directions in editing changes. The final overlap scores are defined as the Z-score of these ratios across all RBP pairs for each cell line. Global direction of editing regulation. We tested whether there exists a sig- nificant bias in the direction of editing changes (higher or lower relative to con- trols) caused by the knockdown of an RBP using a bootstrap sampling approach (Figs. 2, 3, and 5). For each RBP-knockdown sample, we obtained the total number of differentially edited sites (n) and the fraction of these differentially edited sites with increased editing level upon knockdown (r). We then randomly sampled n sites from all testable sites of the same RBP-knockdown dataset and calculated a similar fraction ðr" i Þ. We repeated this random sampling process 100,000 times to obtain an empirical distribution of the ratios: r" ¼ r" 1 ; r" 2 ; ¼ ; r" 100;000. The z- score of r was therefore defined as z ¼ r%b r" σr" where b r" and σr" were the mean and standard deviation of r*, respectively. Finally, the empirical p value of r was cal- culated by comparing to r*. For TARDBP (Fig. 2c), we additionally tested the significance of change in the global editing levels for all testable sites. We performed a similar test as described above, but by randomly sampling sites from all testable sites of all RBP knockdown datasets in the same batch as TARDBP. WGCNA clustering. To examine whether subsets of RBPs function similarly in regulating RNA editing, we carried out a clustering analysis of RBPs using the Weighted Gene Co-expression Network Analysis58. This method finds networks (modules) of nodes based on their topological overlap. For each cell line, the nodes of the WGNCA network consisted of all the RBPs with knockdown data. The edge scores between the nodes (i.e., RBPs) were calculated using pairwise correlation (bicorrelation as recommended by WGCNA) between their differential editing levels between knockdown and controls. We employed WGCNA to create signed networks, which required a soft threshold of 12 to satisfy scale-free topology36. Modules in the resulting dendrograms were then examined manually (Supple- mentary Fig. 6). eCLIP-seq analysis. eCLIP-seq data of 126 and 109 RBPs in K562 and HepG2 cells, respectively, were adapter-trimmed and de-multiplexed59. For each RBP, we obtained eCLIP-seq data from two biological replicates and one size-matched input control59. To accommodate potential Alu-binding proteins whose eCLIP reads may not align uniquely, the eCLIP data were analyzed using a step-wise mapping procedure38. Specifically, the reads were aligned to rRNA sequences first. This step helps to control for spurious artifacts possibly caused by reads derived from rRNA. Those that did not align to rRNAs were retained and aligned to the Alu sequences located in RefSeq genes. This step allows up to 100 multiple alignments per read, maximizing the number of reads that map to Alu elements. Subsequently, reads that did not map to Alu sequences were aligned to the human genome (hg19), where only uniquely-mapped reads were retained. All the alignments were performed by the STAR aligner60 with ENCODE standard parameters (as specified in the STAR manual). All alignments were required to be end-to-end without soft- clipping. eCLIP peaks were called using a Poisson model38 by requiring a Bonferroni-corrected p value cutoff of 0.01. Next, we examined whether the distance between differentially edited sites upon an RBP knockdown and the eCLIP peaks of the RBP is significantly closer than expected by chance. For each differentially edited site, we calculated its distance to the closest eCLIP peak within the same gene. differentially edited sites in genes that do not have an eCLIP peak were discarded. As control sites, we used known editing sites from the REDIportal database7 that satisfy the following: ≥15 combined total read coverage from the two replicates; located in the same gene as the differentially edited site; not identified with edited reads in any dataset of our study. For ADAR1, we used non-REDIportal A’s as random controls, instead of known editing sites. For each RBP, we randomly selected the same number of control sites as that of differentially edited sites and calculated the distance between a control site and the closet eCLIP peak within the same gene. We repeated this process 200 times to generate 200 sets of controls. The distances of each set of controls to eCLIP peaks were visualized via empirical cumulated distribution function (eCDF), similarly for the distances of the actual differentially edited sites to eCLIP peaks. Next, we calculated the area under the curve (AUC) of each distance eCDF and compared the AUC corresponding to differentially edited sites and those resulted from the 200 sets of control sites. It is expected that smaller distances lead to larger AUCs. Thus, to determine whether the differentially edited sites were significantly closer Directional agreement score. For each pair of RBPs tested in the same cell line, we took the union of their associated differentially edited sites and further retained only those sites that are testable in both RBP knockdown datasets. Testable sites were defined as those with ≥5 total reads per replicate, and with ≥10% editing level in either knockdown or control. Using these editing sites, we asked whether the directions of editing changes upon knockdown of the two RBPs are concordant by calculating the directional agreement score. Specifically, for each of the above differentially edited site, we labeled it as + or − if its change in editing level upon RBP knockdown is a positive or a negative value, respectively. For sites with the same label for both RBPs, a +1 agreement score was assigned. Otherwise, a score of −1 was given. If the editing site is differentially edited in only one of the two RBP knockdowns, a score 0 was given. The final directional agreement score of a pair of RBPs is defined as the average value of the score of each included editing site in this analysis. The directional agreement score of the same RBP between K562 and HepG2 was calculated similarly. Co-immunoprecipitation. Cells were maintained with DMEM supplemented with 10% FBS and 100 U mL−1 penicillin/streptomycin at 37 °C and 5% CO2. Ten million cells were collected and lysed in 1 mL non-denaturing lysis buffer at pH 8.0, containing 20 mM Tris-HCl, 125 mM NaCl, 1% NP-40, and 2 mM EDTA sup- plemented with complete protease inhibitor cocktail. Extracted proteins were incubated overnight with DROSHA antibody (Bethyl Laboratories, A301-886A) at 4 °C; precipitation of the immune complexes was performed with Dynabeads Protein G (Thermo Fisher Scientific, 1003D) for 4 h at 4 °C, according to the manufacturer’s instructions. After immunoprecipitation, the beads were washed three times with the lysis buffer at 4 °C and eluted from the Dynabeads using elute buffer (0.2 M glycine, at pH 2.8). Twenty microliters were loaded onto the gel and the samples were processed by SDS-polyacrylamide gel electrophoresis (SDS- PAGE) and analyzed by Western blot. The following antibodies were used for the Western blots: ADAR1 antibody (Santa Cruz, sc-73408) and DROSHA antibody (Bethyl Laboratories, A301-886A). The HRP-linked secondary antibodies were used and the blots were visualized with the ECL kit (GE, RPN2232). Constructs, transfection, luciferase reporter assay. TDP-43 ChIP peak regions were cloned into a firefly luciferase reporter pGL3 vectors (Promega). The pSV40- Renilla vector (Promega) encoding the Renilla luciferase reporter gene Rluc (Renilla reniformis) was used for transfection efficiency. Transfections were per- formed with the use of Lipofectamine 3000 (Invitrogen). HepG2 cells were seeded into 12 well plates at a density of 2.0 × 105 cells per well the day before transfection. For each well of cells 1.0 μg of the pGL3 constructs were co-transfected with 0.1 μg of the pSV40-Renilla vectors. The transfected cells were collected after 48 h. Luciferase activities were measured with the Dual-Luciferase Reporter Assay Sys- tem (Promega, E1910). To normalize for transfection efficiency, the reporter activity was expressed as the ratio of firefly activity to renilla activity. For each construct, three independent experiments were performed in triplicate. Code availability. Scripts for differential editing analysis (and related results) are available at https://github.com/gxiaolab/RNA_editing/tree/master/RBP_regulation. Data availability All data sets used in this study can be obtained from the ENCODE project website at http://www.encodeproject.org. We used shRNA RNA-Seq and eCLIP-Seq datasets in HepG2 and K562 cells with release dates between October 2014 and January 2017. The data underlying the main figures are available in Supplementary Data 1. Received: 2 July 2018 Accepted: 13 December 2018 References 1. Axel, B., Anita, M. & Stefan, B. RNA editing. FEMS Microbiol. Rev. 23, 297–316 (1999). 2. Shaw, J. M., Feagin, J. E., Stuart, K. & Simpson, L. Editing of kinetoplastid mitochondrial mRNAs by uridine addition and deletion generates conserved amino acid sequences and AUG initiation codons. Cell 53, 401–411 (1988). 3. Nishikura, K. A-to-I editing of coding and non-coding RNAs by ADARs. Nat. Rev. Mol. Cell Biol. 17, 83–96 (2016). 4. Bentley, D. L. Coupling mRNA processing with transcription in time and space. Nat. Rev. Genet. 15, 163–175 (2014). 5. Esther Hsiao, Y.-H. et al. RNA editing in nascent RNA affects pre-mRNA ARTICLE COMMUNICATIONS BIOLOGY | https://doi.org/10.1038/s42003-018-0271-8 埼玉大学 理・分子生物 高橋朋子 200822 ENCODE3勉強会@zoom
- 8. 専⾨分野 209件の回答 ウイルス学若⼿ネットワークによる統計 ウイルス学の 研究集会に ウイルス学を 専⾨としない⼈が 多く参加している オンラインだからこそ①︓普段は参加しない学会に 参加できる → 他分野の⼈の話を聞ける 話を聞いてもらえる 職位/学年 205件の回答 ⼤学教員 学⽣ （博⼠） ポスドク 学⽣ （修⼠） 学⽣ （学部⽣） その他
- 9. オンラインだからこそ②︓誰がいるのかわからない 専⾨分野 209件の回答 ウイルス学若⼿ネットワークによる統計 職位/学年 205件の回答 ⼤学教員 学⽣ （博⼠） ポスドク 学⽣ （修⼠） 学⽣ （学部⽣） その他 ウイルス学の 研究集会に ウイルス学を 専⾨としない⼈が 多く参加している ウイルス学若⼿研究集会2020も ENCODE3勉強会も 参加登録約200⼈ → 誰に向かって発表したんだろう...? 想定外の⼈に発表を聞かれる
- 12. 〜まとめ〜 コロナ渦での研究者間コミュニケーション ・ 気軽に連絡する習慣があれば、新規ネットワーク形成は可能 ある程度は ・ ヒトとヒトの繋がりが“⾒えない” 発表しない/発⾔しないと “⾒えない” ので ⾃分が“なにもの”なのか⾃ら述べる（発表をするべき） ・ 直接会いたい⼈がいっぱいいる（早く会えたらいいのに...）