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Rucli S, Descostes N, Ermakova Y, Chitnavis U, Couturier J, Boskovic A, Boulard M. Functional genomic profiling of O-GlcNAc reveals its context-specific interplay with RNA polymerase II. Genome biology 2025 26(1) 40128797
Abstract:
How reversible glycosylation of DNA-bound proteins acts on transcription remains scarcely understood. O-linked β-N-acetylglucosamine (O-GlcNAc) is the only known form of glycosylation modifying nuclear proteins, including RNA polymerase II (RNA Pol II) and many transcription factors. Yet, the regulatory function of the O-GlcNAc modification in mammalian chromatin remains unclear.
O-GlcNAc proteins:
YTDC1, MYC, PO5F1, PO2F1, TBP, SOX2, TYY1, TET1, TET2, SIN3A, KLF4, CTCF, HCFC1, NF2L1, SMAD3, ZN281, RAF1, BRD4, NRF1
Species: Mus musculus
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Hou C, Zhang H, Deng J, Wang X, Byers S, Levi M, Pak DTS, Moremen KW, Pei H, Hart GW, Ma J. Comprehensive Evaluation of Cleavable Bioorthogonal Probes for Site-Specific O-GlcNAc Proteomics. Molecular & cellular proteomics : MCP 2025 24(10) 40885482
Abstract:
O-linked β-N-acetylglucosamine (O-GlcNAc) modification (i.e., O-GlcNAcylation) on proteins is an essential modification in physiology and pathology. Although O-GlcNAcylation is functionally critical, its analysis has been challenging. Despite the existence of a number of methods developed in the past years, which one(s) might have the best performance is largely unclear. To that end, we conducted a rigorous comparison of several cleavable bioorthogonal biotin-alkyne probes which showed promise for sensitive O-GlcNAc proteomics. In brief, we developed chemoenzymatic labeling/click chemistry-based analytical workflows for O-GlcNAc proteomics by utilizing four cleavable bioorthogonal probes, including photocleavabe-biotin-alkyne (PC-biotin-alkyne), dialkoxydiphenylsilane-biotin-alkyne (DADPS-biotin-alkyne); 1-(4,4-dimethyl-2,6-dioxocyclohex-1-ylidene)ethyl-biotin-alkyne (Dde-biotin-alkyne), and diazobenzene-biotin-alkyne (Diazo-biotin-alkyne). The analytical performance of these probes was evaluated with synthetic O-GlcNAc peptides and then benchmarked by using mouse brain lysates for O-GlcNAc proteomics. Besides providing valuable technical insights into O-GlcNAc proteomics methods, our work yielded an unprecedented O-GlcNAc proteome depth in the mouse brain. In total, 2906 O-GlcNAc sites were unambiguously assigned on 878 proteins. Among them, 1611 sites were newly identified, including 138 O-GlcNAcylated tyrosine residues. Our work will help guide the selection/development of O-GlcNAc proteomics methods for future studies, provide an invaluable resource for functional elucidation of protein O-GlcNAcylation in brain biology, and yield critical insights into tyrosine O-GlcNAcylation.
O-GlcNAc proteins:
QSER1, TANC2, ZEP3, MA7D2, CKAP5, AMRA1, CAMP1, LZTS3, AJM1, MA7D1, FRPD1, RPGP1, UBR4, SKT, BCORL, AGRIN, TITIN, SVEP1, ARI1A, SPAS1, PHRF1, PTPRS, SCN2A, DLGP4, EP300, RBM25, ILDR2, CTTB2, PTPRZ, NLRC5, CCDC6, SHAN1, SET1A, PARP4, PRR12, TENS1, I2BP2, AKP13, C2CD2, ARI1B, ZC3HD, ARID2, NUMA1, PDZD7, SC16A, SYGP1, TPR, BICRA, SI1L3, PLGT3, DPYL2, EMD, STXB1, AKAP1, CLOCK, DCTN1, NUMBL, DBIL5, SYPL1, M3K5, SCRB2, ATN1, NOTC2, VIAAT, HAP1, CTND2, PITM1, OX2G, REPS1, AKAP2, ACK1, CNTP1, CAC1B, SYUA, PI51C, ATX2, E41L2, PDLI1, ULK1, UBR1, HCN4, KDM6A, ZN106, PDE8A, PPT1, ZFR, HCN2, HCN1, CTBP1, BSN, TOM1, AKA10, HIPK1, SYN1, LGMN, TPP1, THY1, LAMC1, MBP, ALDOA, GCR, CATL1, EGR1, HCK, ENPL, KCC4, NFL, NFM, ITB1, RC3H2, MAMD1, ATX1L, CATB, TAU, LAMP1, DMD, KCC2A, ITPR1, CNTN1, NCAM1, AT1B2, HSPB1, MAP1B, G3P, ATF2, PPIA, CATD, BASI, COF1, NFH, BIP, HEXB, MTAP2, MAG, CYTC, EMB, GRIA1, GRIA2, RS2, RGRF1, KCC2B, PABP1, C5AR1, AIMP1, DPOA2, RAB23, NMDE1, NMDZ1, FMR1, FOXK1, STAT3, EAA2, EGR3, RAD52, ITAV, CBP, AINX, NEDD4, STT3A, RP3A, EPB41, RFX1, SOX2, LMNA, MPIP1, INPP, DHI1, ARSB, VATA, DVL1, ADCY7, DBX1, E41LA, ARNT, SOX1, ATX1, RD23B, 3BP1, AMRP, CX6B1, CTBP2, MAZ, WFS1, PCBP3, PTPA, KCNN2, FOXP1, TB10A, TB182, GMEB2, KCNH8, CAPAM, RHG39, YTHD1, RPC2, PI5PA, MRTFB, DOCK4, IRPL1, MYPR, ABI2, GBB1, RAB3A, VAMP2, KCNA2, KCNJ3, ZHX1, DCC, NFIX, NCOA1, RGRF2, USP9X, TP53B, NACAM, LYAG, IRS2, TNIK, WNK1, G3BP2, ARG28, MPRIP, CAC1A, NPAS2, GRM1, XRN1, SHPS1, NEO1, G3BP1, NFIB, RLA2, GABPA, CBPE, NMDE2, NMDE3, NOTC1, CTNB1, PLAK, S30BP, ZEP1, ENAH, KCNB1, RCN1, PGBM, EMAL1, LG3BP, TLE3, MITF, SSRP1, CHD8, TRIO, TANC1, RELCH, CDK12, MA6D1, F171B, SHRM4, PHAR1, GSK3A, PSD3, MLXIP, NELL1, ESP1, PLBL2, PDLI7, PRC2C, MILK2, YETS2, SRSF6, FUBP2, SRBP2, GSE1, F117B, WDR62, FOXK2, CARL3, DIP2B, WNK2, LIMC1, TNR6C, DAB2P, AGAP2, ZEP2, ZSWM8, AAK1, TEN4, TNR6A, CAMKV, MTCL1, PKHA7, COBL1, GRIN1, PRRC1, MINY4, FCHO2, SNX21, LIGO2, MRCKA, KSR2, GRM5, ARMX5, ELAP2, GARL3, 5NTC, PACS2, STOX2, UBN1, ABL2, OXR1, DSCL1, CDV3, PHAR4, ANR28, LRC47, SRRM1, EME2, LIN54, TAB3, STB5L, NEXMI, JCAD, NYNRI, NUFP2, UNKL, PRSR1, OSBP2, SMG7, LRRK2, RBM27, PHF12, CYFP2, TM1L2, ANR40, CCD42, SYNRG, RPGP2, NACAD, LHPL4, EPAB2, LMTK3, SIN3A, SRC8, ICAM5, LAMA2, ITF2, CAPR1, NCOR1, FOXG1, LAMA5, NCOA2, LAMC2, IL18R, NAB1, ASTN1, SPIN1, PAPOA, HCFC1, SAP, NELL2, APC, PGCB, ZN638, AP180, FXR1, GRID2, GRID1, PACN1, HIRA, RAI1, MAFK, NPM, NOTC3, CSPG2, M3K7, DAG1, RO52, SN, SPTB2, TAF6, SPEG, ASPP1, SRBS1, DBNL, SH3G1, TLE4, SP4, IF4G2, MINT, ZYX, OMGP, MEF2D, TFE3, PAN3, HECAM, SF01, SYN2, TBR1, DHSO, CGT, CH058, SBNO1, CRTC1, BEGIN, K1549, GIT1, SLAI1, PKP4, SYMC, CDK13, GBA2, SH3R1, PREX1, JHD2C, HECD1, MOR2A, ABLM3, TBC12, ARMX2, CE170, LAR4B, RHG21, HELZ, MEG10, SCAF8, LIGO3, ZZZ3, F135A, FBX41, SPKAP, RPRD2, WWC2, ZN532, DPP10, TAF9B, S23IP, IF4G1, RBM26, NSD3, SNX19, FHOD1, FKB15, MTSS2, BCR, AHDC1, AAKB2, PTN23, LPPRC, PAPD7, MFF, PIGS, TRAK1, PHLB1, KMT2D, RN220, DLGP3, RA54B, GMIP, WASC2, ERC2, KCC2D, NFRKB, ALEX, MAGI1, CENPE, DNMBP, GGYF2, TEX2, PF21A, KDM3B, FNBP4, CNOT1, LARP1, NU188, SYNE1, IF2A, UB2R2, CMYA5, SEM6D, SOX11, ASAP2, HUWE1, SMAP2, PLPR3, PRC2B, C2CD5, TPPP, MACOI, AMPH, ATX2L, PRC2A, TMM94, PP6R1, MAP6, MCAF1, DAAF9, SI1L2, LRRC7, ERBIN, PHF24, R3HD2, NAV3, AGRL1, DEND, AUXI, RERE, SNPH, MADD, RIMB2, PUM1, NU214, SEPT9, SESD1, CBPM, SRA1, EPN1, AKNA, HYDIN, UBN2, AGFG2, CHST2, T106B, C2C2L, REPS2, WNK3, DDHD1, CNKR2, BCAS1, ZN598, SHAN2, PKHL1, S2611, ZFYV1, NRCAM, DLG1, MAST4, RHG32, GPHB5, RN214, LPP, MYPT2, TB10B, CSTP1, SP130, ZC3HE, DLGP2, ZC21A, ZNT6, SUN2, EME1, TNR6B, BAIP2, ABLM2, NCEH1, LRFN3, SHC2, SEN34, FAT3, DMXL2, GORAB, CLAP2, K1671, FAKD3, LIPA2, CNOT4, RALYL, SRRM2, TOX4, PAMR1, F163B, GEPH, CREST, KCC1D, GRIN3, LARP4, Z385B, IFFO1, OSBL6, CC169, TENR, YTHD3, STON2, TM266, POGZ, DOC10, ZHX2, EPC2, SWAHC, ZHX3, SI1L1, SH3R3, FRS2, RBM14, CNOT2, MOR2B, HYCC2, ANK2, ELFN1, TM163, DIDO1, SMAG1, SYNPO, BCAS3, VCIP1, BAKOR, TAB1, SCYL2, NED4L, MEF2C, ASPP2, TENS2, F193A, OGT1, CHERP, NAV1, SYNJ1, RPGF2, EP400, PHC3, DPYD, VP37A, EPN2, P66A, PDLI5, ANM5, DOCK3, PLXB1, DNER, SPAT2, SCAM1, SAM14, ZBT20, PHYIP, RTN1, HS12A, C2D1A, UNC5A, PACS1, TRI68, BRD3, LS14A, AGFG1, MATR3, DEN1A, I2BPL, PO121, ABLM1, MRTFA, RPTOR, PLCE1, SPNS1, CACL1, KCNC4, DC1L1, MTSS1, SPART, LRC42, ZN445, RFIP5, IGSF8, BRD8, WIPI1, CDK8, PP6R2, SHLB2, CS047, NTNG2, PP14C, STAB2, LUZP1, RBM12, STAB1, OTU7A, SC6A8, ULA1, CLPT1, MAVS, GRAP1, SGIP1, PI3R4, PHIP, SIR2, GOLI, AMOT, AGAP3, WASF3, P66B, CCG8, TAF9, ZCH14, MCR, SFPQ, WDR13, UBAP2, SMAP1, NCOA5, CXXC5, FRS3, SPS2L, FUBP1, SH319, ZFN2B, VPS36, DLG2, DYH8, DCP1A, YTHD2, PTBP2, SRGP2, SRGP1, BMP2K, DYST, LRP1, SYUB, ALS2, TRFE, GPS2, CLIP1, WAC, SPRE1, MED1, NRBP, NPTXR, GGT7, GORS2, NONO, TAB2, DPP3, EPN4, RNF34, GAK, DDAH2, ZN281, HGS, RB6I2, RIMS1, ANR17, RTN4, RRBP1, ZN318, TRI33, MZT2, PCYOX, NECP1, FLIP1, NRX1A, SNX2, DDAH1, YIF1B, NOPC1, CYGB, GFOD2, TPD54, CEP97, CD37L, SSBP3, SARNP, SP2, UB2V2, DLGP1, NDUV2, SH24A, FIP1, ST1C2, F135B, TM263, CNPY3, RM12, BTBDH, AL7A1, PLIN3, MYPT1, LNEBL, DCAF6, KC1D, CRIP2, TSC1, NBEA, TCF20, CPSF1, DPYL5, RIMS2, ZN704, RBP2, RTN3, SPN90, SP6, GILT, CLD12, ELF2, TSSC4, LRP1B, NUDT3, CATR, PPR3F, NUP50, TULP4, ORC3, ATR, HYOU1, ADRM1, FMN2, NCOA6, BAG3, MINK1, ZN207, PHC2, SRCN1, ASAP1, SON, SALL2, LIMD1, TBL1X, APBB1, PLEC, MACF1, ULK2, ADDB, ADDA, PCX1, GOGA5, NDRG2, MAGD1, MAP1A, QKI, PCLO, GAB1, MAGL2, FBX6, NPAS3, HIPK2, SH2D3, CATJ, YLPM1, CELR2, RHG07, GUAD, FOXO1, TAGL3, ADA22, AKA12, TEN1, TEN3, NCOR2, ATRN, COR1B, SR5A3, GANP, NFAT5, ASAH1, GSK3B, DEMA, E41L3, CARM1, JIP1, KCNH3, MAGI2, FXR2, SYUG, CLIP2, PALM, ITSN1, ITSN2, ZO2, DYR1B, APCL, BAG6, DPP6, MTMR1, MECP2, SE1L1, E41L1, GRIA3, HOME1
Species: Mus musculus
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Liu X, Cai YD, Hou C, Liu X, Luo Y, Mendiola AJP, Xu X, Luo Y, Zheng H, Zhao C, Chen CH, Zhang Y, Xiang YK, Ma J, Chiu JC. O-GlcNAcylation of nuclear proteins in the mouse liver exhibit daily oscillations that are influenced by meal timing. PLoS biology 2025 23(9) 40997131
Abstract:
The liver circadian clock and hepatic transcriptome are highly responsive to metabolic signals generated from feeding-fasting rhythm. Previous studies have identified a number of nutrient-sensitive signaling pathways that could interpret metabolic input to regulate rhythmic hepatic biology. Here, we investigated the role of O-GlcNAcylation, a nutrient-sensitive post-translational modification (PTM) in mediating metabolic regulation of rhythmic biology in the liver. We observe daily oscillation of global nuclear protein O-GlcNAcylation in the liver of mice subjected to night-restricted feeding (NRF) using label-free global O-GlcNAc proteomics. Additional site-specific O-GlcNAc analysis by tandem mass tag mass spectrometry further supports temporal differences in O-GlcNAcylation by revealing day-night differences. Proteins involved in gene expression are enriched among rhythmically O-GlcNAcylated proteins, suggesting rhythmic O-GlcNAcylation may directly regulate the hepatic transcriptome. We show that rhythmic O-GlcNAcylation can also indirectly modulate nuclear proteins by interacting with phosphorylation. Several proteins harboring O-GlcNAcylation-phosphorylation interplay motif exhibit rhythmic O-GlcNAcylation and phosphorylation. Specifically, we show that O-GlcNAcylation occurs at a phospho-degron of a key circadian transcriptional activator, circadian locomotor output cycles kaput (CLOCK), thus regulating its stability and transcriptional output. Finally, we report that day-restricted feeding (DRF) in the nocturnal mouse significantly alters O-GlcNAcylation pattern. Whereas global O-GlcNAcylation analysis indicates dampening of global O-GlcNAcylation rhythm in mice fed under DRF, site-specific analysis reveals differential responses of O-GlcNAc sites when timing of food intake is altered. Notably, a substantial number of O-GlcNAcylation sites exhibit inverted day-night profiles when mice are subjected to DRF. This suggests the dysregulation of daily nuclear protein O-GlcNAcylation rhythm may contribute to the disruption in liver transcriptome previously observed in DRF condition. In summary, our results provide new mechanistic insights into metabolic regulation of hepatic transcriptional regulators via interplay between O-GlcNAcylation and phosphorylation and shed light on the deleterious effects of improper mealtimes.
O-GlcNAc proteins:
A0A075B680, A0A087WQ44, A0A087WSN6, A0A0A6YVV8, A0A0B6VMB2, A0A0F7QZE4, A0A0G2JGY6, A0A0R4J092, A0A0U1RNL9, A0A1I7Q4G8, A0A1N9PTV1, A0A1Y7VP67, A0A286YCY7, A2A654, ZMYM4, TM201, MED14, A2ADB1, A2AJ72, S35D1, BCORL, A2AQR4, A2ATN3, MGAP, KANL3, PHRF1, B1AR09, B1ASA5, B2RQG2, B2RR24, B2RT41, B2RUQ2, EP300, RBM25, B7ZNL9, D3YWX2, D3Z0K6, D3Z2U7, E9PUF4, E9PUH7, FIBA, E9PV38, SET1A, PARP4, PRR12, E9Q1A5, E9Q1M6, ICE1, E9Q3L4, ANR11, ARI1B, SETD2, YTDC1, ZC3HD, ARID2, E9Q7G1, E9Q9V3, E9Q9Y2, E9QAN9, E9QAP7, E9QKL0, E9QMD3, E9QNA7, F6R9G0, F6T8X6, BICRA, G3UVU2, G3X8Q1, G3X928, G3X961, G3X972, G3X9Q0, PCF11, G5E896, H9KV00, ERR1, GTPB1, HNF6, CLOCK, GLU2B, ATN1, IMA3, KLF12, CALU, AF10, ZN143, SP3, KDM6A, ZN106, ZFR, CCNK, PIAS1, LGMN, SP1, IGHG3, CFAH, EGR1, ITB1, ATX1L, CATB, ITPR1, B4GT1, HNF1A, PGH1, A1AT2, NFYA, PO2F1, 3BHS3, HNF1B, CEBPB, CELF1, RXRA, VTNC, NKTR, SUH, ANT3, G6PC1, FOXA1, FOXK1, STAT3, CBP, FKBP2, FOSL2, RFX1, LMNA, STS, MAT1, PON1, CEBPA, ATX1, RD23B, KMT2A, FUS, PAXB1, LMA2L, MRTFB, SUMO2, PP1B, RS11, SMD3, NFYB, SUMO1, ZHX1, TIAR, TBX3, NFYC, ATF1, ERG, NFIB, RBBP6, GABPA, CREB1, S30BP, NFIA, ZEP1, SPA3M, PPA5, CLUS, GATA4, CHD8, CDK12, Q3T9J2, KHDC4, Q3TGN5, PRC2C, CIART, K22E, YETS2, Q3U1M7, LMF1, FOXK2, PUF60, RREB1, ZEP2, UD3A1, ZCCHV, PRRC1, SFSWA, PRD10, ERMP1, Q3UXF4, TMED1, ZBT45, Q569X9, LIN54, TASO2, RESF1, ZN652, NUFP2, KDM6B, Q5PRE9, Q5RIM6, RBM27, UTP18, Q5SUT0, MED13, Q5SXC4, SFR19, UIMC1, A1CF, SIN3A, CSK21, CAPR1, MEF2A, RBBP7, KLF3, NCOA2, USF1, CTCF, GATA6, TS101, HCFC1, ZN148, HIRA, LASP1, RAI1, MAFK, PRG2, SPTB2, SSXT, TAF6, UD19, NUP62, UD11, MEF2D, TIF1A, USF2, CDK13, JHD2C, HECD1, Q6DI81, SCAF8, NOMO1, FND3B, Q6NXL1, ZMIZ1, NSD3, UGGG1, ALG8, AHDC1, PTN23, PIGS, NUP98, NFRKB, GNAS1, ONEC2, FNBP4, CNOT1, NU188, SPCS3, PICAL, HUWE1, CPEB4, PRR14, ATX2L, NACC1, MCAF1, KANL1, NU214, PR40B, UBN2, TNC18, UBP2L, ZN598, Q80ZX0, DDX42, LPP, TET3, E41L5, SP130, ZC3HE, SUN2, EST2E, NCEH1, ARI5B, EMSY, TM260, RFOX2, TM209, KMT2C, ASPH, SRRM2, NUP54, CPSF7, TOX4, IFIX, CREST, Z385B, PIGT, PGLT1, YTHD3, KAT6A, ASXL2, ZN609, POGZ, SREK1, ZHX2, ZHX3, P20D1, MBNL2, RBM14, PIAS2, CNOT2, ITCH, DIDO1, EPC1, SCYL2, G6PE, TCRG1, BCOR, CCAR1, Q8CHB3, ADNP2, BICRL, EP400, PHC3, P66A, FWCH1, PDLI5, NUP42, ZMIZ2, BTD, UD3A2, ESRP2, TAF10, ZBT20, Q8K154, GT251, ALG3, BRD3, I2BPL, PO121, SF3A1, EST2A, SF3B4, Q8R084, ZBT44, MTSS1, TMED4, ZC3HA, UBQL1, NUP58, BRD8, ATX7, STAB2, RBM12, RBPS2, MED25, MAVS, ALG12, HNRL1, CDIPT, SRSF4, P66B, TAF9, MCR, SFPQ, MBOA5, UBAP2, SMAP1, NCOA5, RBM47, CREL1, SC16B, BAZ2A, RBM5, RISC, ALS2, BCL7B, TMCO1, SYDC, CIC, MED15, WAC, MED1, GORS2, RBM10, ZN281, MLXPL, ANR17, ZN318, TRI33, PCYOX, NECP1, RBM33, SSRA, CREL2, PINX1, INT12, SP2, PHF14, SUN1, APMAP, FIP1, AP2B1, RPN2, LMAN2, AKAP8, MYPT1, RSRC1, EIF3F, Q9EQC8, ERAP1, SALL1, Q9ERL0, RBP2, RTN3, PALLD, TF2H2, ANM1, NUP50, HAKAI, HYOU1, ELOV1, ZN207, DOPP1, CCNT1, TBL1X, PO210, VKGC, QKI, UBQL2, HIPK2, COP1, PR40A, FOXO1, PIGN, MAN1, GANP, ENTP5, NFAT5, CARM1, FOXO3, FBLN5, IF2H, Q9Z1A1, DEAF1, HTAI2, HNRPF, ITPR2, S4R1W8, V9GX43
Species: Mus musculus
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Hao Y, Li X, Qin K, Shi Y, He Y, Zhang C, Cheng B, Zhang X, Hu G, Liang S, Tang Q, Chen X. Chemoproteomic and Transcriptomic Analysis Reveals that O-GlcNAc Regulates Mouse Embryonic Stem Cell Fate through the Pluripotency Network. Angewandte Chemie (International ed. in English) 2023 62(17) 36852467
Abstract:
Self-renewal and differentiation of embryonic stem cells (ESCs) are influenced by protein O-linked β-N-acetylglucosamine (O-GlcNAc) modification, but the underlying mechanism remains incompletely understood. Herein, we report the identification of 979 O-GlcNAcylated proteins and 1340 modification sites in mouse ESCs (mESCs) by using a chemoproteomics method. In addition to OCT4 and SOX2, the third core pluripotency transcription factor (PTF) NANOG was found to be modified and functionally regulated by O-GlcNAc. Upon differentiation along the neuronal lineage, the O-GlcNAc stoichiometry at 123 sites of 83 proteins-several of which were PTFs-was found to decline. Transcriptomic profiling reveals 2456 differentially expressed genes responsive to OGT inhibition during differentiation, of which 901 are target genes of core PTFs. By acting on the core PTF network, suppression of O-GlcNAcylation upregulates neuron-related genes, thus contributing to mESC fate determination.
O-GlcNAc proteins:
AMRA1, SETX, SKT, BCORL, AGRIN, MGAP, ARI1A, CHD6, PHRF1, ZCH24, EP300, KIF7, KI67, CE350, ANR11, NUMA1, TPR, MORC3, TAF4B, KMT2B, EMD, AKAP1, TCOF, DCTN1, MNT, NCOA3, ATN1, ECP3, DPOD2, CTND2, PIAS3, AF10, ACK1, GET3, DSG2, ESS2, ATX2, PDLI1, ULK1, BARD1, KDM6A, ZN106, NSD1, ZFR, HIPK1, SETB1, LAMC1, MYCN, GCR, EGR1, RC3H2, ATX1L, DERPC, K2C8, HSPB1, JUND, FGFR1, G3P, ATF2, COF1, HEXB, VIME, PO5F1, CBL, CCNB1, PO2F1, RS2, NFKB1, MAX, PABP1, NEDD1, PTN12, FMR1, ELK1, FOXK1, STAT3, SOX15, PLIN2, CBP, NEDD4, YAP1, RFX1, SOX2, LMNA, ROA1, S1PR2, ARNT, RD23A, PLTP, KMT2A, KLF16, FOXP1, TB182, GMEB2, SENP1, YTHD1, MRTFB, DOCK4, STIM1, TBX3, NCOA1, ERF, SIAE, NACAM, ATF1, WNK1, G3BP2, DNLI3, G3BP1, RLA2, GABPA, S30BP, ZEP1, ENAH, SOX13, CAPR2, APLP2, CLUS, TLE3, GATA4, MITF, CHD8, ZCH18, TANC1, CDK12, SAP25, LIN41, MLXIP, HROB, VRTN, CO039, PDLI7, SMCA4, PRC2C, MILK2, MIDN, YETS2, PBIP1, FUBP2, TFPT, SRBP2, GSE1, F117B, ZN865, WDR62, QRIC1, FOXK2, RREB1, TNR6C, DAB2P, TNR6A, RHG17, PKHA7, COBL1, FCHO2, TET1, ARMX5, GARL3, TET2, CDV3, PHAR4, C2CD3, LIN54, NPA1P, TAB3, TASO2, RESF1, NUFP2, UNKL, COBL, KDM6B, PRSR1, SMG7, RBM27, PHF12, ZDBF2, PUR4, SYNRG, UIMC1, SIN3A, NFAC2, SRC8, SKIL, ELF1, KLF4, NCOR1, KLF3, NCOA2, FOXD3, PAPOA, HCFC1, P3C2A, SIX4, ZFHX3, TOB1, AP180, GLI3, ATRX, MAFK, NPM, M3K7, DAG1, SPTB2, TAF6, TIF1B, SPT6H, SH3G1, ARI3A, TLE1, TLE4, IF4G2, MINT, ZIC3, ZYX, NUP62, PHC1, TFE3, TIF1A, SF01, DAZL, RBL1, KNL1, BCL9L, SBNO1, SLAI1, PKP4, CDK13, SH3R1, JHD2C, HECD1, ARMX2, LAR4B, RHG21, HELZ, SCAF8, UTF1, PKHG2, NIPBL, CCD66, F135A, RPRD2, WWC2, ZN532, KRBA1, TAF9B, RBM26, INT1, BCR, AHDC1, PTN23, PAPD7, KDM3A, KMT2D, CHD4, RN220, NUP98, NFRKB, GGYF2, LCOR, TEX2, PF21A, KDM3B, FNBP4, CNOT1, LARP1, RHG26, NU188, CNDD3, SPAG5, HUWE1, SMAP2, CPEB3, MYCB2, PRC2B, PRR14, MACOI, ATX2L, CKP2L, PRC2A, MCAF1, SI1L2, KANL1, ERBIN, R3HD2, RERE, PUM2, PUM1, NU214, WNK4, TCAM1, SAS6, CAMP3, UBN2, TNC18, AGFG2, WNK3, ZN598, CTIP, SHAN2, NANOG, DDX42, RHG32, VGLU3, LPP, TET3, MYPT2, IF4B, CNO10, MISSL, TB10B, CARF, TGO1, ZN879, SP130, ZC3HE, ZNT6, SUN2, TNR6B, ARI5B, BNC2, KAT6B, KMT2C, CLAP2, CNOT4, SRRM2, TOX4, GEPH, SYP2L, LARP4, KANK2, SALL4, YTHD3, TOIP2, KAT6A, ASXL2, POGZ, TAF5, ZHX2, EPC2, SI1L1, CND2, RBM14, SUCO, CNOT2, DIDO1, SMAG1, LENG8, CDAN1, DPPA4, LRIF1, VCIP1, MB214, TAB1, SCYL2, ASPP2, LS14B, SYEP, F193A, BCOR, OGT1, SUGP1, NAV1, SYNJ1, ADNP2, RPGF2, BICRL, EP400, PHC3, VP37A, EPN2, P66A, PDLI5, ELYS, ZBT20, ANLN, AGFG1, MATR3, CASC3, I2BPL, PO121, ALMS1, SF3A1, GRHL2, ATF7, CACL1, DC1L1, MTSS1, SPART, TDIF2, HBP1, NUP58, RFIP5, BRD8, WIPI1, CDK8, CS047, ATX7, NUP35, LUZP1, RPAP2, NDC1, MAVS, AMOT, CSKI2, P66B, TAF9, IPO4, ZCH14, UBAP2, NCOA5, FUBP1, RBM47, AJUBA, VPS36, DCP1A, EGLN2, YTHD2, SRGP2, GRHL1, BCL7B, P4R3B, PLRG1, WAC, TRPS1, MED1, ACATN, NRBP, RP25L, NONO, TAB2, EPN4, DDAH2, NOG2, ZN281, HGS, NASP, ARIP4, ANR17, ZN318, TRI33, MZT2, ZWINT, ECD, YIF1B, ROA0, DHRS7, TPD54, SSBP3, PSRC1, SARNP, BCL9, SP2, NOP56, SH24A, FIP1, PLIN3, MYPT1, KC1D, TCF20, TOR3A, SALL1, ZN704, RBP2, UBE4B, TBX20, AFF4, RBCC1, 4ET, PALLD, ELF2, TSSC4, NUDT3, HAKAI, ADRM1, NCOA6, FANCA, GIT2, BAG3, TOB2, ZN207, SON, TBL1X, PLEC, MACF1, GOGA5, QKI, GAB1, DMRT1, YLPM1, PCM1, RHG07, TAF7, FOXO1, ADA23, AKA12, UXT, MAN1, NCOR2, AKT3, COR1B, TNIP1, GANP, DEMA, CARM1, RGAP1, ITSN2, ZO2, KLF5, ADNP, ARI3B, BCL3, SE1L1, E41L1, ZN292
Species: Mus musculus
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Burt RA, Dejanovic B, Peckham HJ, Lee KA, Li X, Ounadjela JR, Rao A, Malaker SA, Carr SA, Myers SA. Novel Antibodies for the Simple and Efficient Enrichment of Native O-GlcNAc Modified Peptides. Molecular & cellular proteomics : MCP 2021 20 34678516
Abstract:
Antibodies against posttranslational modifications (PTMs) such as lysine acetylation, ubiquitin remnants, or phosphotyrosine have resulted in significant advances in our understanding of the fundamental roles of these PTMs in biology. However, the roles of a number of PTMs remain largely unexplored due to the lack of robust enrichment reagents. The addition of N-acetylglucosamine to serine and threonine residues (O-GlcNAc) by the O-GlcNAc transferase (OGT) is a PTM implicated in numerous biological processes and disease states but with limited techniques for its study. Here, we evaluate a new mixture of anti-O-GlcNAc monoclonal antibodies for the immunoprecipitation of native O-GlcNAcylated peptides from cells and tissues. The anti-O-GlcNAc antibodies display good sensitivity and high specificity toward O-GlcNAc-modified peptides and do not recognize O-GalNAc or GlcNAc in extended glycans. Applying this antibody-based enrichment strategy to synaptosomes from mouse brain tissue samples, we identified over 1300 unique O-GlcNAc-modified peptides and over 1000 sites using just a fraction of sample preparation and instrument time required in other landmark investigations of O-GlcNAcylation. Our rapid and robust method greatly simplifies the analysis of O-GlcNAc signaling and will help to elucidate the role of this challenging PTM in health and disease.
O-GlcNAc proteins:
IQIP1, A0A0A6YWG7, A0A0G2JF55, A0A0N4SW93, A0A0R4J060, A0A0U1RPL0, A0A140LIW3, A0A140T8K9, A0A1B0GS41, A0A1B0GS91, A0A1D5RMI8, A0A1L1M1J8, A0A1L1SR84, A0A1N9NPH8, A0A1Y7VNZ6, A0A286YDB3, A0JNY3, A2A482, A2A654, TANC2, LZTS3, AJM1, BCORL, A2AUD5, A2AWN8, B1ASA5, B1ATC3, B1AUX2, B2RQL0, CSPP1, B2RY58, B7ZNA5, CTTB2, D3YU22, D3YUV1, D3YWX2, D3YZ21, SHAN1, D3Z5K8, E0CXZ9, E9PUL3, PRRT2, E9PUR0, E9PV26, E9PVY8, SET1A, E9Q0N0, E9Q3E2, NU153, E9Q4K0, ARI1B, SETD2, E9Q6H8, E9Q6L9, E9Q828, E9Q9C0, E9Q9Y4, E9QAQ7, E9QAU4, E9QAU9, E9QKI2, E9QLZ9, E9QM77, F2Z3U3, F6RQA2, SYGP1, F7C376, BICRA, F8VQL9, F8WIS9, G3UZM1, G3X8R8, G3X928, RFIP2, H3BKF3, H3BKP8, H9KV00, J3QNT7, DPYL2, PRDX6, MNT, NUMBL, PEX5, BMPR2, CTND2, PITM1, ACK1, CAC1B, SYUA, DSG2, SPT5H, E41L2, SP3, KDM6A, CPNS1, ZFR, HCN1, CTBP1, BSN, STAM2, SYN1, MBP, EGR1, NFL, NFM, ITB1, RC3H2, ATX1L, RL7A, MAP1B, VIME, EIF3A, RGRF1, PABP1, FOXK1, EAA2, CBP, RFX1, SOX2, KPYM, CTBP2, GCP3, TB182, GMEB2, PI5PA, DOCK4, PCBP1, LIPA3, RS3, PAX6, KCNJ3, PP2BA, TBA4A, STAM1, NCOA1, CXB6, WNK1, PSME2, WBP2, SHPS1, NRSN1, CTNB1, PLAK, S30BP, ZEP1, YES, CAPR2, MITF, GRD2I, Q0VF59, HDX, MA6D1, F171B, ZFHX2, MLXIP, PDLI7, PRC2C, CIART, YETS2, SRBP2, Q3U2K8, GSE1, RREB1, WNK2, DAB2P, ZEP2, AAK1, TNR6A, GRIN1, SRBS2, GRM5, Q3UZG4, RBM44, Q3ZB57, PHAR4, RESF1, Q5EBP8, UNKL, VP13A, COBL, KDM6B, PRSR1, Q5RIM6, SMG7, RBM27, TM1L2, Q5SVJ0, Q5SXC4, SIN3A, GAS7, CAPR1, KLF3, SIX4, AP180, GRID2, PACN1, LASP1, RAI1, NOTC3, SALL3, SPTB2, ARI3A, NUP62, PHC1, TFE3, PAN3, TIF1A, SF01, SYN2, SBNO1, CRTC1, RIPR1, GIT1, PKP4, ABLM3, ARMX2, CE170, Q6AXD2, NIPBL, FBX41, RPRD2, WWC2, Q6P1J1, Q6P5E3, UGGG1, SPRE3, Q6P9N8, AHDC1, PTN23, TRAK1, DLGP3, NYAP1, DHX29, NFRKB, MAGI1, Q6XZL8, CNOT1, SYNE2, IF2A, PLPR4, PLPR3, CCNT2, PRC2A, MAP6, MCAF1, RERE, NU214, SESD1, C2C2L, CNKR2, SLIK5, RHG32, LPP, NELFA, C42S2, TB10B, TGO1, RFOX3, SP130, ANS1B, ZC3HE, ZC21A, BAIP2, KAT6B, RELL2, LIPA2, CNOT4, TOX4, GASP2, CREST, KDM4A, GRIN3, KAT6A, ZN609, PAK5, A16L1, SI1L1, SH3R3, SKA3, RBM14, Q8C5J0, CNOT2, WDR26, UBA6, ANK2, DIDO1, SYNPO, VCIP1, FHI2A, NUP88, NED4L, SET1B, TENS2, OGT1, NAV1, STAU2, AFG32, S4A8, ZBT20, HS12A, GLT18, UNC5A, AGFG1, FRRS1, KCNQ3, PO121, T2FB, MTSS1, Q8R2E1, NUP35, MAVS, SGIP1, HNRL1, PP16B, CCG8, SFPQ, UBAP2, NCOA5, AJUBA, DCP1A, TWF1, ALS2, ETFD, GRIP1, GORS2, NONO, ZN281, CT2NL, RN111, ANR17, PPP6, RBM7, CYGB, SARNP, DLGP1, SUN1, TM263, GON4L, PLIN3, MYPT1, NBEA, ZN704, RBP2, ARHG7, RTN3, NUDT3, TULP4, Q9JIZ5, PAR6G, SCAM5, PRG4, ZN207, SRCN1, ASAP1, DREB, ULK2, ADDA, PCLO, UBQL2, FBX6, PCM1, SYT7, CRY2, FOXO1, MAST1, LYPA2, TEN3, GANP, DEMA, E41L3, ZO2, BAG6, E41L1, RM40, GRIA3, S4R294, V9GWU7, V9GX40
Species: Mus musculus
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Chuh KN, Batt AR, Zaro BW, Darabedian N, Marotta NP, Brennan CK, Amirhekmat A, Pratt MR. The New Chemical Reporter 6-Alkynyl-6-deoxy-GlcNAc Reveals O-GlcNAc Modification of the Apoptotic Caspases That Can Block the Cleavage/Activation of Caspase-8. Journal of the American Chemical Society 2017 139(23) 28528544
Abstract:
O-GlcNAc modification (O-GlcNAcylation) is required for survival in mammalian cells. Genetic and biochemical experiments have found that increased modification inhibits apoptosis in tissues and cell culture and that lowering O-GlcNAcylation induces cell death. However, the molecular mechanisms by which O-GlcNAcylation might inhibit apoptosis are still being elucidated. Here, we first synthesize a new metabolic chemical reporter, 6-Alkynyl-6-deoxy-GlcNAc (6AlkGlcNAc), for the identification of O-GlcNAc-modified proteins. Subsequent characterization of 6AlkGlcNAc shows that this probe is selectively incorporated into O-GlcNAcylated proteins over cell-surface glycoproteins. Using this probe, we discover that the apoptotic caspases are O-GlcNAcylated, which we confirmed using other techniques, raising the possibility that the modification affects their biochemistry. We then demonstrate that changes in the global levels of O-GlcNAcylation result in a converse change in the kinetics of caspase-8 activation during apoptosis. Finally, we show that caspase-8 is modified at residues that can block its cleavage/activation. Our results provide the first evidence that the caspases may be directly affected by O-GlcNAcylation as a potential antiapoptotic mechanism.
O-GlcNAc proteins:
A2A4A6, A2A5R8, GPTC8, SPD2B, A2ACG7, A2AFQ9, A2AFW6, A2AG46, CKAP5, A2AH75, A2AJ72, MA7D1, A2AL12, A2AMW0, A2AMY5, TPX2, PPIG, LAS1L, A5A4Y9, A6PWC3, A6PWK7, UBP36, B1AT03, B1AT82, B1AU75, B2RQG2, OTUD4, B7ZCP4, B7ZP47, D3YUW8, D3YWF6, D3YWK1, D3YX62, SAFB1, D3YXM7, D3YZ06, D3YZP6, D3Z069, D3Z158, D3Z3F8, D3Z6W2, E0CYM1, E9PUH7, E9PVM7, E9PWG6, E9PWV3, E9PWW9, E9PY48, E9PYT3, E9PZM7, E9Q066, E9Q2X6, NU153, E9Q450, E9Q4K7, E9Q4Q2, KIF23, BD1L1, NUMA1, E9Q7M2, E9Q986, E9Q9E1, E9Q9H2, E9QKG3, E9QKG6, E9QKZ2, E9QLA5, E9QP49, E9QP59, E9QPI5, F2Z3X7, F6S5I0, F7AA26, F7BQE4, FARP1, F8VQ93, F8VQC7, F8VQE9, F8VQK5, F8WI30, G3UZ44, G3UZX6, G3X8R0, G3X8Y3, G3X928, G3X963, G3X972, G3X9V0, G5E896, G5E8E1, H3BJU7, H3BK31, H3BKK2, H7BX26, I1E4X0, I7HIK9, J3QNW0, DPYL2, GTPB1, AKAP1, TCOF, AIP, HDAC1, RL21, GSH0, KIF1C, DHX15, SC6A6, IF6, ILK, ATX2, NMT1, E41L2, DHB12, SRPK1, ZN326, ZFR, PARG, SPD2A, SP1, CASP8, HPRT, LDHA, G6PI, TYSY, RIR1, GNAI2, ITB1, 4F2, H2B1F, MAP1B, HMOX1, LEG1, G3P, KS6A3, COF1, GNAO, IFRD1, VIME, UBL4A, CBX3, CXA1, CATA, IMDH2, IL1RA, MCM3, CDK4, NKTR, FKBP4, CBX2, HMGB2, AIMP1, KAP3, MP2K1, SYWC, KIF4, NEDD1, DPOLA, RANG, UBP4, PTN11, RAB18, PTN1, PTN12, LDLR, DNLI1, CAP1, STAT3, STA5B, PURA, ALD2, RAGP1, NEDD4, STT3A, ALDH2, GSHR, GFPT1, PCY1A, MCM4, ICAL, PLCB3, CDN2A, HDGF, UBP10, KPYM, CCHL, IDHP, DDX6, GOGA3, COX17, ACTN4, GCP3, TB182, EIF3E, ABCE1, PFD3, 1433E, RAP1A, RS25, TCTP, DNJA1, HMGB1, IF5A1, RS17, RS12, UB2L3, HXD13, HDAC2, ELAV1, TP53B, CASP3, PYRG1, TCPB, STIM2, SRSF3, CSRP2, SPTC2, BOP1, SMAD4, M4K4, HNRL2, MARK3, LARP7, CNN2, PP4R2, PEPD, CDCA2, Q3TFP0, GUAA, PDE12, Q3TL72, PRC2C, NOL9, FUBP2, TRADD, CTU2, ZN865, Q3U4W8, Q3UG37, NAT9, NOL8, Q3UJQ9, SC31A, NCBP1, LRRF1, DDX17, LRC47, JIP4, EHMT1, CA050, AAPK1, NSRP1, Q5RL57, Q5SQB0, TENS3, PUR4, Q5UE59, SRC8, SAMH1, KHDR1, GRB10, HELLS, SPB6, RIPK1, CAPR1, ASNS, LAP2A, CDC37, TS101, SNTB2, FNTA, BAP31, PLPP1, FSCN1, FXR1, DDX5, ATRX, DDX3Y, DDX3X, TGFI1, DBNL, SH3G1, CYTB, SMAD2, NDRG1, ZYX, SQSTM, TPP2, ZN512, LAR4B, F120A, CNDG2, NOP58, LTV1, Q6NV52, Q6NXL1, Q6NZD2, ANKL2, Q6P5B5, XPO1, KIF15, FHOD1, TXLNA, PTN23, JUPI2, NUDC1, TACC1, UBE2O, LARP1, ACAP2, 2AAA, MTCH2, ZN503, CYFP1, HNRPQ, SPAG7, DEK, ACTN1, ATX2L, CKP2L, ZN516, ERBIN, SEPT9, PGRC2, Q80VB6, PI42B, ZN598, SAFB2, Q80ZX0, DLG1, LPP, PEF1, IF4B, FTO, TIPRL, Q8BH80, MISSL, ERC6L, CARF, PRUN1, NUP93, FBX30, HBAP1, AHSA1, RCC2, IPO5, SYLC, CKAP4, MAP11, PALM2, CPNE3, SENP7, CSN7B, NSD2, DPP9, Q8BWW3, KANK2, PXK, PIGT, ITPK1, NHLC2, MAP1S, GWL, PKHH2, CND2, THOP1, SEP11, SKA3, CA198, SEP10, AROS, UBA6, LIPB1, SMAG1, Q8CCM0, ZN276, NAA30, SNX8, SYEP, OGT1, GNL3, PDLI5, FERM2, AGO2, HMCS1, AMERL, SCNM1, DNM1L, NEK9, ANLN, EDC3, MATR3, CHAP1, MEPCE, ERF3A, CC137, TDIF2, VPS18, RFC3, MCMBP, HEXI1, LUZP1, SNP47, TMX1, MAVS, UBXN4, Q8VCQ8, ACSF2, PARN, VIGLN, PSMD2, NAA40, F1142, ZNG1, PAXI, SFPQ, CPIN1, RAB14, IPYR2, PUS7, CSDE1, PIP30, RABE2, CISD1, Q91X76, DUS3L, KCC1A, TTC1, SRGP2, SNX18, RISC, HNRLL, Q921K2, PP6R3, LRC59, UBXN1, DBR1, KCC2G, Q924B0, WAC, SMC6, PAWR, SIAS, STML2, PSIP1, NXF1, PDXD1, NONO, PLST, RRAGC, VMA5A, MAOM, DCTN2, ZN281, CT2NL, GRPE1, ABD12, NU155, OGFR, NPM3, NOP16, GLOD4, DUT, MTAP, IFM3, CYB5B, PAF15, PSMD9, WIPI3, SKA2, VATG1, CHSP1, LRC40, RANB3, SMC1A, MFR1L, ARHGP, DDX47, TBC15, PPIL4, MPPB, CYBP, TECR, SERB1, ZCHC8, SPCS2, Q9CZP3, CD37L, SSBP3, MMS19, MGRN1, ARPIN, HNRPM, SYRC, MCES, Q9D4G5, ATAD1, F162A, TRIR, IPYR, PHF10, ARFG3, ORN, BOLA1, CNN3, KAP0, PLIN3, AKAP8, XRN2, GNAI3, PUR6, RAI14, SENP3, ARFG1, SIL1, VPS35, DGCR8, SYCC, ELP4, LIMA1, XPO2, RBP2, RTN3, PALLD, TMOD3, STK3, COPB, NUP50, DDX21, SH3L1, DDX20, MBNL1, BAG3, GKAP1, ZN207, TRXR1, PPCE, CAF1A, LIMD1, NDRG3, DNJC7, NFU1, COPG1, NUBP1, SMAP, DEST, ACOT9, PR40A, FOXO1, FIZ1, NFKB2, KAD2, AKA12, PRKRA, PDC6I, CHIP, COR1C, VAPA, NDKM, E41L3, TAGL2, CARM1, MTNB, BCL10, IF2G, P5CS, COG1, MD2L1, EIF3G, SAE2, ILF3, TRIP6, USO1, BAZ1B, HNRPF, KEAP1
Species: Mus musculus
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Myers SA, Panning B, Burlingame AL. Polycomb repressive complex 2 is necessary for the normal site-specific O-GlcNAc distribution in mouse embryonic stem cells. Proceedings of the National Academy of Sciences of the United States of America 2011 108(23) 21606357
Abstract:
The monosaccharide addition of an N-acetylglucosamine to serine and threonine residues of nuclear and cytosolic proteins (O-GlcNAc) is a posttranslational modification emerging as a general regulator of many cellular processes, including signal transduction, cell division, and transcription. The sole mouse O-GlcNAc transferase (OGT) is essential for embryonic development. To understand the role of OGT in mouse development better, we mapped sites of O-GlcNAcylation of nuclear proteins in mouse embryonic stem cells (ESCs). Here, we unambiguously identify over 60 nuclear proteins as O-GlcNAcylated, several of which are crucial for mouse ESC cell maintenance. Furthermore, we extend the connection between OGT and Polycomb group genes from flies to mammals, showing Polycomb repressive complex 2 is necessary to maintain normal levels of OGT and for the correct cellular distribution of O-GlcNAc. Together, these results provide insight into how OGT may regulate transcription in early development, possibly by modifying proteins important to maintain the ESC transcriptional repertoire.
O-GlcNAc proteins:
A2A653, A2A654, D0VLQ4, E9QAP7, PRDX6, MAFK, ZFR, MYB, EGR1, SOX2, EBP, S30BP, TLE4, CDK12, ZFHX3, Q2TBA4, YETS2, Q3TWV0, TNR6A, Q3UY82, RESF1, SIN3A, NCOR1, TAF6, MINT, SBNO1, CDK13, JHD2C, RPRD2, NUP98, NFRKB, PF21A, KDM3B, NU188, MCAF1, NU214, Q80WR0, SP130, SALL4, POGZ, RBM14, CNOT2, DIDO1, EP400, PHC3, AGFG1, NUP35, P66B, MED15, ZN281, ZN318, TRI33, LMAN1, SP2, PIFO, TCF20, RBP2, ELF2, YLPM1, NCOR2
Species: Mus musculus, Homo sapiens
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