[No authors listed]
Protein-RNA interactions are fundamental to core biological processes, such as mRNA splicing, localization, degradation, and translation. We developed a photoreactive nucleotide-enhanced UV crosslinking and oligo(dT) purification approach to identify the mRNA-bound proteome using quantitative proteomics and to display the protein occupancy on mRNA transcripts by next-generation sequencing. Application to a human embryonic kidney cell line identified close to 800 proteins. To our knowledge, nearly one-third were not previously annotated as RNA binding, and about 15% were not predictable by computational methods to interact with RNA. Protein occupancy profiling provides a transcriptome-wide catalog of potential cis-regulatory regions on mammalian mRNAs and showed that large stretches in can be contacted by the mRNA-bound proteome, with numerous putative binding sites in regions harboring disease-associated nucleotide polymorphisms. Our observations indicate the presence of a large number of mRNA binders with diverse molecular functions participating in combinatorial posttranscriptional gene-expression networks.
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NBPF10, TSFM, LRPPRC, RBM12, G3BP1, SUGP2, MBNL2, CEBPZ, TRIM28, RBM7, RBM6, RBM5, ALYREF, MPHOSPH10, EIF1, DDX39A, HNRNPR, MRPS31, POP7, SRRM1, SF3B4, AKAP8, LOC400927-CSNK1E, SAP18, EIF1B, SF3A1, CDKN2A, ADAR, NPM3, RACK1, NSA2, ADARB1, RBM14, EMG1, NXF1, SYNCRIP, MYBBP1A, DDX17, CHERP, NOP56, PRPF8, IGF2BP1, IGF2BP3, IGF2BP2, KHDRBS3, KHDRBS1, CELF1, CELF2, KIF1C, SRSF10, UTP14A, CPSF4, TCERG1, RNPS1, SUB1, SRSF8, SF3A3, HNRNPA0, EBNA1BP2, CKAP4, ASCC3, GCN1, SF3B2, NUDT21, CPSF6, DDX52, CHD2, DUSP14, DIDO1, NUPL2, HNRNPUL1, KRR1, LSM6, PSIP1, STRAP, SUPT16H, MRPL3, ATXN2L, LARP4, DDX42, PDAP1, U2AF2, WBSCR22, KCTD12, CIRBP, MRPL54, FTSJ3, EXOSC6, CHCHD1, CLK3, CLTC, HIST4H4, ZC3H18, MSI2, MRPL10, RAVER1, C1orf131, RBM45, CPEB2, SRSF12, RPP25L, SREK1, PARP1, CS, CSNK1E, CSTF1, CSTF2, CSTF3, RC3H1, LSM14B, C2orf15, SRFBP1, RBM33, NOP9, ZNF579, DDX1, DDX3X, DDX5, DDX6, DHX8, DHX9, DDX10, DHX15, DHX36, DNM1, DYNC1H1, EEF1A1, AGO3, EEF2, EIF1AX, EIF2S1, EIF4A1, EIF4A2, EIF4B, EIF4E, EIF4G2, EIF5, EIF5A, ELAVL2, ELAVL1, IBA57, APOBEC3F, ERH, FBL, EWSR1, FARSA, FASN, ZCCHC24, FAU, MRPL21, PATL1, HNRNPA3, HNRNPUL2, ALDOA, CASC3, XRN2, PUF60, CPEB3, FASTKD2, DHX30, RALY, NCBP2, MAPRE1, SNW1, PDCD11, ACIN1, SPEN, CNOT1, SNRNP200, RBM34, SMG1, RRP1B, PEG10, ZC3H13, GPATCH8, FLNA, FLNB, LARP4B, FAM120A, ZC3H4, RRS1, PRRC2C, RRP12, ABCF1, ZC3H7B, CSTF2T, ZCCHC11, FMR1, SYNE1, U2SURP, LARP1, PUM2, RRP8, TARDBP, HARS2, SF3B1, PES1, MACF1, R3HDM1, SRRM2, RBFOX2, GTPBP4, ZNF346, MKRN2, GSPT2, IFIT5, FUS, YTHDF3, XRCC6, FAM133B, LSM4, MTO1, DCAF13, NOL11, FAM98A, ZNF385A, SYF2, PNISR, KIAA1429, NGDN, SPATS2L, PTCD1, GIGYF2, LSM14A, CCDC9, CHTOP, PRPF31, SERBP1, NOC2L, RSL1D1, ERAL1, GNL3, AGO1, DAZAP1, AATF, GDI2, PABPC1, AKAP8L, TRUB2, SND1, STAU2, AGO2, LSM1, LSM3, DIMT1, RBMX, TNRC6A, ZNF638, UTP20, MCAT, APOBEC3C, GOT2, C11orf31, FAM98B, ZNF326, RPUSD3, RPL7L1, MRPS28, MRPL13, ZC3H7A, MRPL15, MRPL22, DROSHA, CFAP20, GRSF1, GTF2F1, ABT1, GNL2, RBM15B, TRA2A, PURG, GLTSCR2, H1F0, HIST1H1C, HIST1H1D, HIST1H1E, HSD17B10, HDAC2, HDLBP, DNTTIP2, ANXA7, ANXA11, HMGB1, HMGB2, HMGB3, HMGN2, DDX51, HNRNPA1, HNRNPA2B1, HNRNPAB, HNRNPC, HNRNPD, HNRNPF, HNRNPH1, HNRNPH2, HNRNPH3, HNRNPK, HNRNPL, HNRNPU, HOXB6, PRMT1, APEX1, HSPA8, HSPA9, HSP90AA1, HSP90AB1, CCDC137, HNRNPCL1, ILF2, ILF3, EIF3E, JUN, ARF1, KPNB1, KPNA2, TNPO1, IPO5, LIN28B, RBM12B, VSIG8, RPSA, LBR, MEX3D, MYO18A, CAPRIN1, MAGOH, MAP4, MAZ, MBNL1, MDH2, MFAP1, MOV10, MSI1, MYH9, MYO5A, HNRNPM, NAP1L1, NCBP1, NCL, NDUFV3, RPL10A, NFX1, SNU13, NOP2, NONO, CNOT4, NOVA1, NOVA2, NPM1, YBX1, P4HB, PRDX1, MYEF2, PCBP1, PCBP2, RPS27L, YARS2, MRPL2, MRPL4, MRPS7, UTP18, UTP11, MRTO4, DDX47, MRPL27, MEX3C, ARL6IP4, NGRN, CRNKL1, EIF3L, NIP7, DDX41, YTHDF2, C9orf114, NOP16, RTCB, PPHLN1, ZCCHC17, LARP7, ESF1, SRRT, NOP58, LUC7L2, SF3B6, MRPS23, ZFR, LSM8, WBP11, LUC7L3, ZAK, PFN1, PIN4, EXOSC10, PNN, POLR2A, POLR2B, POLRMT, GAR1, RBM27, MRPS21, XRN1, RBM47, DHX29, PUS7, RC3H2, OTUD4, PPIA, PPIB, ANKHD1, NSUN2, ALKBH5, YTHDF1, TRMT10C, SARS2, TRNAU1AP, FAM120C, PPP1CC, NOL8, PTCD3, MRPL20, CXorf57, SAMD4B, MAGOHB, HEATR1, RBM28, LARP1B, PPP1R10, MTPAP, MRM3, RAVER2, NAT10, PSPC1, IMP3, BRIX1, PEF1, WDR33, STRBP, NCBP3, HIST2H4B, RBM38, LYAR, PRPF40A, DDX27, NSUN5, RBM22, CCAR1, DDX28, MBNL3, ZC3H15, PRKDC, RCC2, NKRF, EIF2AK2, PCDHGA9, YLPM1, MEPCE, KYAT3, PPAN, EIF4ENIF1, ZC3HAV1, PNO1, DUS3L, RARS2, UTP3, DDX24, REXO4, ZNFX1, PTBP1, SCAF4, LRRC47, XPO5, NUFIP2, FBRSL1, NCOA5, SUGP1, CCAR2, LSM2, PURA, PURB, PTBP2, PWP2, CACTIN, RBM25, RAN, RBBP6, RBM3, RBM4, RBMS1, RBMS2, UPF1, MRPS35, FASTKD5, ELAC2, RP9, RPL3, RPL4, RPL5, RPL7, RPL7A, RPL8, RPL10, RPL11, RPL12, RPL15, RPL17, RPL18A, RPL21, RPL22, RPL23A, RPL24, RPL26, RPL27, RPL30, RPL27A, RPL29, RPL35A, RPL37A, RPL36A, RPLP0, MRPS12, RPS2, RPS3, RPS3A, RPS4X, RPS5, RPS7, RPS8, RPS10, RPS12, RPS13, RPS14, RPS15, RPS15A, RPS16, RPS17, RPS18, RPS19, RPS20, RPS23, RPS24, RPS25, RPS26, RPS27, RPS27A, RPS28, RRBP1, SAFB, ATXN2, UBE2O, HEATR6, MRPS14, RBM26, SFPQ, TFB2M, SRSF1, SRSF2, PAPD5, SRSF3, SRSF4, SRSF5, SRSF6, NOC3L, SRSF7, TRA2B, NOM1, NUCKS1, MTHFSD, RBM15, DDX31, YTHDC2, PCDH20, MRPL14, MRPS26, MRPS24, MRPS11, MRPS9, MRPS5, MRPL41, MRPL40, MRPL11, MRPL9, MRPL1, MRPL44, UPF3B, RSRC2, SUMO2, SNRNP70, SNRPA, SNRPA1, SNRPB, SNRPC, SNRPD1, SNRPD3, SON, SPTBN1, SRP14, SRP72, SRPK1, SRPK2, SSB, SSBP1, SSRP1, STAU1, SUPT5H, SUPT6H, SUPV3L1, SURF6, BTF3, TBCA, TCOF1, TCP1, TFAM, TIA1, TIAL1, TOP1, TOP2A, CCT3, TSNAX, TXN, U2AF1, UBC, UBA1, UBE2N, UBTF, VCP, EZR, EIF4H, XRCC5, SF1, CNBP, ZNF207, CSDE1, DAP3, DDX50, ERI3, DDX54, METTL16, CCDC86, DEK, NOL12, PRRC2A, C1orf35, DDX39B, HMGN5, NKAP, ZCCHC6, FASTKD1, ZNF768, TEFM, MTERF1, PTCD2, SLTM, ALG13, CPSF7, ZC3H14, MRM1, NOL10, ESRP2, RPF1, CPEB4, PUS1, PRR3, FXR1, PABPN1, ANP32A, TAF15, TDRD3, RCC1L, FIP1L1, AKAP1, SF3A2, TRIM56, LAS1L, SLIRP, CANX, AKAP17A, SMC1A, HIST1H4I, EPPK1, HIST1H4A, HIST1H4D, HIST1H4F, HIST1H4K, HIST1H4J, C11orf68, FAM103A1, HIST1H4C, HIST1H4H, HIST1H4B, HIST1H4E, HIST1H4L, HIST2H4A, GRWD1, RBM4B, SLC25A11, WDR75, UTP15, RPF2, MEX3B, FYTTD1, POLDIP3, NTPCR, LLPH, PYM1, NUDT16L1, MRPL45, CMSS1, SARNP, NIFK, DUSP11, DHX16, ZC3H8, PRRC2B, PHF5A, RPUSD4, PRPF38A, YBX3, PPIL4, ZCCHC3, API5, ZCRB1, HELZ2, UNK, RRP1, KHSRP, PRKRA, NOP14, CDK13, EIF3A, EIF3C, EIF3D, EIF3G, EIF4G3, SRSF9, PNPT1, EDF1, PABPC4, RRP36, FUBP1, DDX18, EIF2S2, PRPF4B, FUBP3, TOP3B, H1FX, RPL14, ZNF598, SART1, DHX57, USP10, PRPF3, FAM50A, RRP9, RPS19BP1, SCAF11, YTHDC1, DDX21, MTDH, NOLC1, MEX3A, NAF1, TBRG4, WDR46, HNRNPLL, SRSF11, EFTUD2, PPIG, ZRANB2, DDX23, QKI, EIF4E2, ROCK2, FXR2, BAG4, APOBEC3B, RBM39, SAFB2, EIF5B, BZW1, PUM1, DHX34, AQR, SECISBP2L, SART3, BCLAF1, EIF4A3, MATR3, DHX38, BMS1, CDK11B, URB1, ZC3H11A, DDX46, CDC5L, UBAP2L, RBM19, G3BP2, HELZ, PUM3, RBM8A, THRAP3, HNRNPDL, PTBP3
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