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Jeon BC, Kim YJ, Park AK, Song MR, Na KM, Lee J, An D, Park Y, Hwang H, Kim TD, Lim J, Park SK. Dynamic O-GlcNAcylation governs long-range chromatin interactions in V(D)J recombination during early B-cell development. Cellular & molecular immunology 2025 22(1) 39627609
Abstract:
V(D)J recombination secures the production of functional immunoglobulin (Ig) genes and antibody diversity during the early stages of B-cell development through long-distance interactions mediated by cis-regulatory elements and trans-acting factors. O-GlcNAcylation is a dynamic and reversible posttranslational modification of nuclear and cytoplasmic proteins that regulates various protein functions, including DNA-binding affinity and protein-protein interactions. However, the effects of O-GlcNAcylation on proteins involved in V(D)J recombination remain largely unknown. To elucidate this relationship, we downregulated O-GlcNAcylation in a mouse model by administering an O-GlcNAc inhibitor or restricting the consumption of a regular diet. Interestingly, the inhibition of O-GlcNAcylation in mice severely impaired Ig heavy-chain (IgH) gene rearrangement. We identified several factors crucial for V(D)J recombination, including YY1, CTCF, SMC1, and SMC3, as direct targets of O-GlcNAc modification. Importantly, O-GlcNAcylation regulates the physical interaction between SMC1 and SMC3 and the DNA-binding patterns of YY1 at the IgH gene locus. Moreover, O-GlcNAc inhibition downregulated DDX5 protein expression, affecting the functional association of CTCF with its DNA-binding sites at the IgH locus. Our results showed that locus contraction and long-range interactions throughout the IgH locus are disrupted in a manner dependent on the cellular O-GlcNAc level. In this study, we established that V(D)J recombination relies on the O-GlcNAc status of stage-specific proteins during early B-cell development and identified O-GlcNAc-dependent mechanisms as new regulatory components for the development of a diverse antibody repertoire.
O-GlcNAc proteins:
MPEG1, CUL4B, DHX8, RHG27, VIR, PNISR, FRPD1, RENT2, LAS1L, ITIH4, THOC2, MMRN1, PYR1, YTDC2, PTPRB, ANR44, RBM25, OSBL8, DAAF5, SAFB1, KI67, DESP, YTDC1, UBE4A, NUMA1, MORC3, HXK2, LEG9, KNG1, UBE3A, DCTN1, DIAP1, U5S1, RL21, PHB2, CPSF2, DHX15, EXOC4, STAG2, AP1B1, PININ, HNRH1, SP100, GP1BA, ITB3, RL35A, SPT5H, DHX9, E41L2, BAZ1A, ZFR, ROA2, PRS6A, FA5, AFAM, COR1A, SP1, C1QR1, COX2, AMY1, CO3, CO4B, B2MG, HBA, HBB1, K1C10, K2C1, CFAB, ALDOA, TBA1B, TBA3, ITAM, K1C18, LDHA, LCK, APOA4, PTPRC, CFAH, TTHY, ANXA2, ALBU, A1AT1, SPA3K, HS90A, TRFL, ENPL, APOE, MDHM, GNAI2, RPB1, ITB1, PDIA1, NUCL, APOA2, PTPRQ, CALM2, EF1A1, 4F2, PARP1, PERM, FINC, HS90B, K2C8, ITA5, ITB2, TCPA, RL7A, GELS, ICAM1, DNMT1, S10A6, RL27A, RS16, RL7, RSSA, LMNB1, ANXA6, RLA0, CD44, LEUK, H12, CN37, AMPE, HS71L, G3P, LAMP2, HSP72, ENOA, PTBP1, PPIA, TPIS, LYZ1, PCNA, PTPRA, BASI, KS6A1, KS6A3, COF1, FAS, THRB, RL13A, BIP, VIME, PLMN, VTDB, A1AT2, CBL, AP1G1, EIF3A, EST1C, ITAL, CD11B, MCM3, RS2, CD19, UBF1, TLN1, EZRI, MOES, KLKB1, H2AX, VAV, NCKP1, MUG1, KIF2A, DPP4, PTN6, FETUA, C5AR1, CEAM1, CD68, ANT3, SYWC, KIF4, DPOLA, RAB5C, RAB18, CD22, TSP1, CALX, RFC1, PRDX1, RL12, RL18, DNLI1, GRP75, DYN2, RL28, MMP9, STAT1, STA5B, EPS15, TCPQ, MSH2, H14, H15, RAGP1, SIPA1, NSF, PRS7, BRCC3, NEDD4, CAPZB, RL6, RL5, RL13, RL36, KSYK, PERE, ROA1, MCM4, MCM5, SAHH, K2C6A, VATA, PA2G4, RAB7A, RL9, ADT2, IMA1, PON1, DPOD1, UBP10, KPYM, STAT6, RL10A, CEBPZ, PIPNB, MSH6, UBP5, ATPB, UBP25, NICA, ACTN4, EF2, OPA1, FOXP1, TPM2, WDHD1, ARPC4, RUVB1, PCBP1, ACTB, IF4A1, RS20, UB2D3, ARF3, RL26, RL27, RL37A, ARF4, HNRPK, RS7, PRS4, RS8, RS15A, RS14, RS23, RS18, RS11, RS13, SMD2, ARF6, PRS10, RS4X, RL18A, RL23A, RS6, H4, VATB2, RAB1A, RAN, RL23, RS24, RS25, RS26, RL30, RL31, RS3, RL8, PROF1, RL40, HSP7C, PHB1, RL22, RACK1, ACTS, TBA4A, TBB4B, 1433F, IMB1, M4K1, PKN1, STIM1, PYRG2, ROCK1, RAD50, PYRG1, TCPH, TCPB, TCPD, TCPE, TCPZ, TCPG, WNK1, RHOG, RL19, H33, BACH2, MCM2, MCM6, RS3A, ANX11, SMRC1, FUMH, ARVC, TBB5, APOA1, A1AT4, TYY1, HNRL2, LYAM3, TOP2A, APOH, TERA, UBA1, PLAK, ATPA, IKZF1, SPA3M, SMRCD, TOP1, RAC2, PYC, IF2P, CBG, ACADS, AMBP, PECA1, SSRP1, ZCH18, K2C80, PSA, PTCD3, NSUN2, EDEM3, MCM9, TMC5, HMHA1, HP1B3, GUAA, H2AV, SMCA4, PRC2C, MIDN, K1C26, K22E, PSMD1, BRE1B, ESYT1, AAK1, RHG17, EDC4, UBP19, GPD1L, ELNE, SC31A, IQGA2, K22O, ITB2L, C1TM, UN13A, PLCH1, PDS5B, CENPJ, DDX46, TR150, A16A1, EHMT1, MCTP2, RBM27, CYFP2, PSME4, MYO1G, LC7L3, PUR4, MYH1, LEO1, SIN3A, XRCC1, ODO1, HNRPD, SAMH1, HELLS, ARHG2, I17RA, PML, 2A5G, PPM1G, CFAI, CERU, CTCF, PRDX2, EZH2, HCFC1, PA1B3, ARHG1, PLSL, A2AP, HSP74, DSG1A, GSLG1, EWS, RAD21, FSCN1, GDIB, DDX5, HS105, ITIH2, ITA6, EI2BD, SERA, KINH, PDCD4, PZP, PRG2, MYH10, MCM7, NPM, PCBP2, CTR9, DDX3X, CD180, SPTB2, SPR1A, TIF1B, TFR1, RU17, SPT6H, NDUA4, IF4G2, MINT, RHG30, H2B1B, TOP2B, TPP2, AT2A3, H2A2C, VINC, PUR2, CLH1, SYMC, GNPTA, PDS5A, CDC5L, CE290, F120A, UBP7, JADE3, K1C42, K2C72, SR140, K2C73, S23IP, IF4G1, RBM26, P4R3A, U520, ABCF1, SMHD1, UGGG1, XPO1, ANO6, KIF15, KIF11, FHOD1, FKB15, PTN23, LPPRC, SMRC2, ECM29, CHD4, PK3C3, NUP98, GMIP, NFRKB, TEX2, UBE2O, KDM3B, CE162, CNOT1, CAND1, LARP1, VIP2, RS9, RL35, RS27L, 2AAA, SND1, ASAP2, IPO8, HUWE1, LC7L2, MBB1A, INT7, CTDP1, PP6R1, ELP1, DCAF1, CLAP1, SCRIB, PUM1, NU214, NAA15, FACD2, FBLL1, UBP2L, SYMPK, SIG10, DDX42, ANFY1, EFTU, TNPO1, ROA3, PLD4, SYAC, S2512, NU107, PTBP3, NRDC, ERC6L, GANAB, SP130, NUP93, SUN2, RCC2, IPO5, EMSY, ODP2, RBGPR, SYLC, SYQ, ECHA, RL24, CLAP2, CNDH2, PB1, FLNA, SYIC, IFIX, CIP2A, GEMI5, UBP47, CTL2, TBCD, POGZ, ANC2, KS6A5, EFL1, LCAP, DOCK8, CND2, IWS1, RBM14, DOCK2, UBA6, MIC60, UFL1, VCIP1, NUP88, NED4L, RPB2, AQR, SMC4, SMC2, SYEP, TCRG1, LONM, OGT1, CHERP, CCAR1, INT5, PYGB, COPA, PLCG2, INT4, EIF3B, BCLF1, K319L, URP2, DNM1L, NEK9, FCHO1, PAF1, IPO11, CND1, MATR3, PLCL2, DP13A, PO121, SF3A1, HNRPL, NU133, EIF3C, BST2, CD177, ADIPL, CDC16, STPAP, LRC8C, ACSF2, EVI2B, MYH9, UHRF1, VIGLN, ADPGK, PSMD2, HNRL1, AT1A1, MICA1, CCAR2, DX39A, SRSF4, K2C79, RFA1, HNRPU, S25A3, RBM39, SEC63, IPO4, SFPQ, ACLY, IF4A3, NDUS1, ATPG, DDX1, UBAP2, HEMO, IPO9, RBM5, PRP6, SMCA5, SP16H, TADBP, SF3B3, SYDC, PP6R3, C1TC, NOP2, PDE2A, KIF2C, K2C5, SIR1, XPO5, SMRD2, ECHB, ARP3, EMIL1, UN45A, ACON, DPP3, HSP7E, GTPB4, ARBK1, SRRT, SF3B1, NU155, RRBP1, DHX30, RL17, NUDC2, 6PGL, COTL1, RM18, TRAP1, AT5F1, RL14, XPOT, PRPS2, RRP44, SMC1A, SMUF1, SMC3, PUR9, SNX2, ROA0, RL11, GARS, RL15, MTREX, MMS19, HNRPM, SYRC, NH2L1, RL34, GRIFN, UB2V2, S10AE, CORO7, STAG1, CUL5, SC23B, CALL3, NOP56, RL4, EF1G, PRP4, QCR2, PELP1, AP2B1, XRN2, NVL, EIF3K, 6PGD, SYF1, EIF3F, XPO7, IPO7, RENT1, BCAP, PESC, ERAP1, VPS35, EHD4, TFP11, XPO2, PKHA2, RBP2, UBE4B, SHIP1, HRG, XPO4, AN32B, GTF2I, DYHC1, STK4, COPB, DDX21, ACINU, FLII, IQGA1, HYOU1, HIP1R, FMNL1, SACS, SART3, GIT2, MY18A, ITA2B, FAK2, CAF1A, K1C17, FETUB, PLEC, PO210, ADDA, PCLO, COPG1, UBQL2, H2AY, ZEB2, GALK1, SC11A, MTA2, PR40A, TIM, MYO1C, INSRR, MD1L1, PDC6I, PFKAP, CXA10, GANP, IF2G, ADNP, P5CS, SAE2, ARI1, DX39B, CLIC1, SYVC, AP3B1, ILF3, USO1, HNRPC, BAZ1B, K1C16, SNUT1
Species: Mus musculus
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Shu XE, Mao Y, Jia L, Qian SB. Dynamic eIF3a O-GlcNAcylation controls translation reinitiation during nutrient stress. Nature chemical biology 2022 18(2) 34887587
Abstract:
In eukaryotic cells, many messenger RNAs (mRNAs) possess upstream open reading frames (uORFs) in addition to the main coding region. After uORF translation, the ribosome could either recycle at the stop codon or resume scanning for downstream start codons in a process known as reinitiation. Accumulating evidence suggests that some initiation factors, including eukaryotic initiation factor 3 (eIF3), linger on the early elongating ribosome, forming an eIF3-80S complex. Very little is known about how eIF3 is carried along with the 80S during elongation and whether the eIF3-80S association is subject to regulation. Here, we report that eIF3a undergoes dynamic O-linked N-acetylglucosamine (O-GlcNAc) modification in response to nutrient starvation. Stress-induced de-O-GlcNAcylation promotes eIF3 retention on the elongating ribosome and facilitates activating transcription factor 4 (ATF4) reinitiation. Eliminating the modification site from eIF3a via CRISPR genome editing induces ATF4 reinitiation even under the nutrient-rich condition. Our findings illustrate a mechanism in balancing ribosome recycling and reinitiation, thereby linking the nutrient stress response and translational reprogramming.
O-GlcNAc proteins:
A0A075B5P4, A0A087WNV1, A0A087WPT1, A0A087WQF8, A0A087WS88, A0A0A0MQM6, A0A0A6YVP0, A0A0A6YY72, A0A0B4J1E2, A0A0G2JFJ6, A0A0G2JFN8, A0A0G2JFY0, A0A0G2JG10, A0A0G2JG59, A0A0G2JG60, A0A0G2JG65, A0A0G2JGL8, A0A0H2UH17, A0A0J9YTU3, A0A0J9YUT8, A0A0J9YUY8, A0A0N4SV00, A0A0N4SV32, A0A0N4SW94, A0A0N5E9G7, A0A0R4J060, A0A0R4J169, A0A0R4J1E3, A0A0R4J1Y4, A0A0R4J260, A1BN54, A1L341, A1L3S7, A2A485, A2A513, A2A5N3, A2A8V8, A2AGK3, LZTS3, A2AM70, A2AMY5, A2APQ6, A2AS44, A2AVJ7, A2AWT6, A2BGG7, KANL3, K1C28, A6X8Z3, A8Y5K6, B0V2N8, B1AU25, TBD2A, THOC2, TPC11, PLXB2, RBM25, B7FAU9, B7ZWM8, B8JK33, B9EHJ3, D3YTT9, D3YUW7, D3YV30, D3YV43, D3YVH4, D3YX49, D3YX64, D3YX85, SAFB1, D3YYT0, D3YZ62, D3YZL1, D3YZT4, D3Z1X3, D3Z2H7, D3Z3E8, D3Z4B0, CCD78, D3Z6N3, CILP2, D6RCG1, E0CY31, E0CYH0, E9PUA5, E9PUJ2, E9PUX0, GCN1, E9PVC6, E9PVG8, KI67, E9PW24, E9PYF4, SET1A, E9PYI8, E9PZW0, E9Q066, E9Q0F0, E9Q0M9, E9Q0U7, E9Q0Y4, E9Q133, E9Q166, E9Q175, E9Q1Z0, E9Q2X6, E9Q3G8, NOLC1, E9Q5F6, E9Q616, MYO1E, E9Q6A9, E9Q6M7, E9Q6T8, E9Q8F0, E9Q9C7, E9Q9H2, E9QA74, E9QAT0, E9QKG6, E9QLM4, E9QN31, E9QNH6, E9QNN1, E9QPE7, E9QPI5, F2Z480, F6S6G6, F6T0G2, F6TFN2, F6TW20, F6WTC8, F6XWD4, F6YRW4, F6YUI5, F7B296, F7C312, FARP1, F8VPX1, F8VQ29, F8WHR6, G3UWP5, G3UWZ0, G3UX48, G3UYD0, G3UYG6, G3UYW3, G3UYZ0, G3X8P9, G3X8Q0, G3X956, SI1L3, G5E839, G5E846, G5E866, G5E879, G5E8C3, G5E8J8, G5E8N3, G5E8T6, H3BJU7, H3BKF6, H3BKM0, H3BKN0, H3BKT5, H3BL49, J3QMC5, J3QNW0, CAN2, ATN1, SRSF5, IMA3, PININ, EIF3D, ATX2, E41L2, UGDH, SP3, IF2B1, ZFR, HIPK1, IGKC, IGHG1, HBA, K2C1, TBA1B, ALBU, HS90A, NUCL, ATX1L, EF1A1, H2B1F, CO1A1, HS90B, TCPA, GELS, HS71L, AP2A2, K1C19, BIP, VIME, MFGM, EIF3A, MCM3, MOES, CTNA1, U2AF2, PDIA3, GRN, PABP1, FKBP4, KIF4, TSP1, GRP75, TKT, BCL6, FOXK1, H14, NEDD4, LMNA, MCM5, K2C6A, IMA1, KPYM, DDX6, ACTN4, EF2, ASXL1, ACTB, ABCE1, RRAS2, H4, HSP7C, CH60, TBA1A, TBB4B, H31, IMB1, TCPB, TCPE, TCPZ, WNK1, H32, MPRIP, G3BP1, TBB5, HNRL2, TOP2A, UBA1, PLAK, IF2P, EPS8, LRIQ1, ZCH18, LMTD2, FA83H, CDCA2, CYTSA, SPP2B, Q3TJ56, K22E, FUBP2, Q3U6F1, Q3U8S1, FOXK2, PUF60, Q3UID0, Q3UJB0, Q3UNN4, SFSWA, K22O, CFA74, Q3UYN2, LRRF1, ESF1, KIF22, Q3V3Y9, Q45VK5, Q4FJZ2, Q4KL80, Q4TU83, PDS5B, DDX17, LRC47, Q52KR6, TR150, NEXMI, JCAD, NUFP2, PRSR1, RBM27, PHF12, UTP18, LC7L3, Q5SUT0, TSR1, MYO1D, Q5U4C5, SIN3A, SRC8, MYL6, STIP1, CAPR1, IMA5, LAP2A, HCFC1, K1C15, SMRD1, FXR1, DDX5, HS71A, SERA, KINH, MYH10, SIN3B, DDX3X, TIF1B, NUP62, K1C12, SQSTM, TOP2B, Q68EM3, CLH1, CDC5L, F120A, CNDG2, NOP58, SCAF8, K1C42, K2C1B, SR140, ZC11A, ABCF1, RRP12, Q6P5B5, UGGG1, XPO1, KIF11, FHOD1, LPPRC, NUP98, Q6PGF5, NEB2, DAPLE, UBE2O, LARP1, NU188, WDR43, 2AAA, Q792Z1, PICAL, UHRF2, MBB1A, Q7TQE2, NU214, WNK4, KIRR1, UBP2L, FLNB, WNK3, Q80ZX0, LPP, ACTBL, P4HTM, MYPT2, HTSF1, IF4B, NU107, WDR3, NOC4L, CE128, NUP93, SUN2, RCC2, EMSY, SYLC, CKAP4, SRRM2, NUP54, PWP2, SYIC, RL1D1, MAP1S, TTC34, SI1L1, RBM14, Q8C872, DIDO1, ATAD2, NUP88, Q8CFQ9, SMC2, UACA, SYEP, TCRG1, OGT1, CCAR1, SLTM, BICRL, P66A, COPA, HMCS1, Q8JZN2, EIF3B, BCLF1, PHLB2, NAT10, ANLN, SDHA, LS14A, MATR3, DDX18, PO121, EIF3L, HNRPL, NU133, EIF3C, ZC3HA, TDIF2, NUP58, CD109, LUZP1, UTP6, MYH9, UHRF1, VIGLN, CCAR2, CUL7, K2C79, Q8VGW3, DHX36, SFPQ, ACLY, DDX1, U3IP2, SYYC, RPN1, YTHD2, BMP2K, SNX18, SMCA5, Q921K2, SF3B3, DDX27, Q921S6, SMTN, PP6R3, K2C5, DEN2B, NXF1, NONO, ACON, NMD3, RTCB, CT2NL, HSP7E, NU155, IF2B3, Q9CPN9, SMC1A, SMC3, CXXC1, GARS, CEP72, SC23B, Q9D6D0, NOP56, FIP1, SPB1, MYPT1, NVL, EIF3F, RAI14, CPSF1, PESC, VPS35, LIMA1, DKC1, PALLD, NUP50, DDX21, FLII, YBOX3, IQGA1, Q9QUK9, CAF1A, K1C17, MAGD1, MTA2, PR40A, MYO1C, COR1C, E41L3, EHD1, WDR46, ZO2, NU160, ADNP, SYVC, Q9Z1R9, BAZ1B, K1C16, SNUT1, S4R2A9, S4R2J9, V9GX87
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, E9Q3G8, 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, NFIA, 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, PICAL, PLPR4, PLPR3, CCNT2, PRC2A, MAP6, MCAF1, RERE, NU214, SESD1, UBP2L, C2C2L, CNKR2, SLIK5, RHG32, LPP, NELFA, C42S2, TB10B, TGO1, RFOX3, SP130, ANS1B, ZC3HE, ZC21A, BAIP2, EMSY, 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, CIC, 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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Qin K, Zhu Y, Qin W, Gao J, Shao X, Wang YL, Zhou W, Wang C, Chen X. Quantitative Profiling of Protein O-GlcNAcylation Sites by an Isotope-Tagged Cleavable Linker. ACS chemical biology 2018 13(8) 30059200
Abstract:
Large-scale quantification of protein O-linked β- N-acetylglucosamine (O-GlcNAc) modification in a site-specific manner remains a key challenge in studying O-GlcNAc biology. Herein, we developed an isotope-tagged cleavable linker (isoTCL) strategy, which enabled isotopic labeling of O-GlcNAc through bioorthogonal conjugation of affinity tags. We demonstrated the application of the isoTCL in mapping and quantification of O-GlcNAcylation sites in HeLa cells. Furthermore, we investigated the O-GlcNAcylation sensitivity to the sugar donor by quantifying the levels of modification under different concentrations of the O-GlcNAc labeling probe in a site-specific manner. In addition, we applied isoTCL to compare the O-GlcNAcylation stoichiometry levels of more than 100 modification sites between placenta samples from male and female mice and confirmed site-specifically that female placenta has a higher O-GlcNAcylation than its male counterpart. The isoTCL platform provides a powerful tool for quantitative profiling of O-GlcNAc modification.
O-GlcNAc proteins:
A0A0A6YVU8, A0A1B0GSG7, RBM47, ZN335, A2A8N0, SBNO1, CNOT1, PHRF1, ZN462, TAGAP, D3YUK0, E9PUR0, E9PVW1, E9PWI7, PARP4, E9PZS2, E9Q2C0, E9Q3G8, E9Q616, BD1L1, E9Q732, ARHG5, E9Q7N9, E9Q842, E9Q9B4, E9Q9Q2, E9QA22, E9QAE1, F6Y6L6, F8VQ29, F8VQM5, J9JI28, PDLI1, SPT5H, TAF4, ARI1A, ABLM1, KMT2D, MYPT1, ZN609, SET1A, SYNEM, PUR4, TNC18, KDM6A, DPOD2, M3K7, TPD54, SYNJ1, ZN207, SRPK2, ACK1, SYUA, MYPT2, KIF1B, HBP1, OGA, VINEX, PLIN3, MAFK, BRD4, PDLI1, KDM6A, SRPK1, N4BP1, ANR17, NCOR1, CREG1, CRTAP, MYO1A, MTR1L, CREG1, TOX4, SUN1, M3K6, PSMG1, SC24B, CNOT4, ABL1, ABL1, EGFR, LAMC1, LMNA, GBA1, GCR, HSPB1, PPBT, RLA2, ITB1, K1C18, K2C8, SAP, CATL1, LAMB1, ENPL, BGLR, NFIC, VIME, SNRPA, ROA1, ATX1L, TGAP1, GLI2, HLAC, CATB, TAU, BIP, FINC, K2C8, TPR, MSH3, ENPL, PO2F1, ATF2, GNS, ZEP1, RS2, MUC1, JUNB, ATF7, CATD, SON, SERPH, NELFE, BIP, ROA2, CBL, IF4B, APC, ARNT, MAP4, TEAD1, RXRA, RXRB, RXRG, CLIP1, AIMP1, HXA11, ELF1, NU214, MP2K2, VATA, CUX1, PBX2, MLH1, STAT3, SSRB, KI67, STT3A, RFX5, LMNA, DPOD2, PAXI, CDK8, YLPM1, NU153, RBP2, TAF6, EMD, PPT1, FXR1, ICAL, HCFC1, AGFG1, NUP98, ATX1, ATN1, PTN5, AF17, DSRAD, AMRP, ACYP2, NU107, ACOT8, S26A1, TB182, YTHD1, ASXL1, PI5PA, RIN3, MRTFB, RL37, KCNA2, RALA, STIM1, PITX1, IF4G2, SRPK2, RENBP, COG7, WNK1, SERF2, RPTN, SPSY, DAB2, RBM10, HNRPU, SPTB2, FOXK2, EWS, MEF2A, SP2, CO7A1, S30BP, NUCB1, ENL, IF4G1, K1C17, TLE3, TLE4, TOP1, SUH, CBG, ACK1, DEMA, AHNK, FOXO1, TROAP, BPTF, NFIA, ROA0, G3BP1, PABP4, ATM, PICAL, MAMD1, RIPK1, STIM1, MTMR1, CUL4B, ASPP2, KLF5, NFYC, CDK13, VEZF1, DSG2, TRI29, UBP2L, SRC8, PUM1, EPN4, RRP1B, NCOA6, DIP2A, MEF2D, NUMA1, R3HD1, KIF14, EBP, RCN1, KS6A1, RBMS2, TAF1C, NCOA2, SF01, JHD2C, MARE1, ELF2, TAB1, ZFHX3, ZYX, ADRM1, CCDC6, TAF9, STX1A, RFX7, QSER1, QRIC1, PRC2C, PBIP1, GSE1, TNR6A, CEAM5, Q3UKP4, COBL1, ARH40, SC31A, PEG3, SRBS2, Q3UU43, Q3UUE0, F91A1, ARBK2, Q497W2, Q4KL65, PHAR4, EPC2, CRTC2, BCORL, BRD10, TGO1, PRC2B, TOIP1, SPG17, SHRM1, ZN362, LRIF1, RHG21, UBAP2, RBM26, RPRD2, ZN318, NCOR1, LAMA5, HCFC1, P3C2A, SAP, AP180, MAFK, SPTB2, SH3G1, ZYX, TSH3, INADL, WAPL, KAZRN, SBNO1, ARID2, DYH17, SAM9L, CDK13, LAR4B, BICRL, RHG21, HELZ, TTLL5, PANX2, PKHG2, NIPBL, LIN54, F135A, RPRD2, IF4G1, SPIC, SCYL2, NFRKB, INT1, ZN182, UGGG1, MDEAS, ZC3HE, RICTR, FIP1, CRTC3, SAS6, MCAF1, BCOR, GGYF2, NU188, CO039, UBN2, HAKAI, ASXL2, SPT6H, DDX46, KDM3B, PICAL, PRC2B, OOG2, ZIC5, NRK, POGZ, MAVS, CLAP1, EMSY, I2BP2, SRGP1, SH3R1, HUWE1, YTHD3, NU214, UBP2L, TMC5B, ZN598, TOPRS, SHAN2, Q80ZX0, ZNF18, Q810G1, BCL9L, LUZP1, PRSR1, DDX42, PALB2, P66A, GNS, LPP, TB10B, TGO1, Q8BIB6, ZN771, ZNT6, AAPK2, CNOT4, SP110, IFFO1, YTHD3, NCBP3, DEFI6, RBM14, CNOT2, CABS1, Q8C6L9, TCAL5, TAB1, SCYL2, ASPP2, PHC3, EPN2, PDLI5, I2BP1, RN135, AHNK2, NAV2, MISP, MGAP, ANKH1, PHAR4, XRN1, PELP1, Q8JZK6, Q8K0U8, AGFG1, TXD11, IL23R, ARHG6, SPART, SPICE, NUP93, CLASR, ZN786, SYNPO, FNBP4, ARFG1, ENAH, TNR6A, PHC3, SP20H, NAV1, VP37A, KMT2C, BD1L1, NUP35, STXB6, KNL1, TCAL3, MTSS1, SPART, NUP35, PUM2, STT3B, ALMS1, GEMI5, WIPF2, MAVS, UTP6, PI3R4, AMOT, P66B, STAG1, PCNP, LMO7, ATX2L, CSKI2, P66B, BBX, TITIN, HNMT, UBAP2, DCP1A, NRIF1, SMG7, RTF1, MAML1, ZN592, LAR4B, TAF4B, SHIP1, DDX17, RENT1, GPKOW, FUBP2, LPP, TTC28, PF21A, INT12, RCN3, CERS2, PDLI5, FUBP3, MY15B, ANCHR, CLP1L, Z512B, ZFR, EP400, NOL4L, RBM14, CIC, MED15, PIGS, DCR1C, SIN3A, MINT, EYA3, TEAD3, ATX2, RFC4, DHX58, ANX13, GORS2, TAB2, EPN4, ANR17, DPH2, WAC, DIDO1, YTHD1, AMRA1, TANC1, TXD12, F133B, RBM33, GPI8, Q9D2U0, ZC21B, FUND2, F162A, APMAP, Q9D809, FIP1, CNPY3, Q9DAV5, Q9DB24, ALG2, PLIN3, MYPT1, WWTR1, Q9EQC8, SALL1, RBP2, GILT, MFF, SP130, APC1, I2BPL, RBNS5, EPC1, ADNP, ZN106, TM245, CPVL, PTN23, WNK1, E41L1, ZHX3, ZN335, PKHG2, CCSE2, CQ10B, MLXIP, PKHA5, RC3H2, TAF9B, ZBT20, NCOA5, ZN532, APMAP, HYOU1, ADRM1, GIT2, BAG3, UBN1, PDLI7, DIAP3, RBM12, CARF, ETAA1, HXC10, TAB2, UGGG1, CDK12, ITSN2, CNOT2, TMEM9, DAPLE, NYAP2, KANL3, SON, LIMD1, KI21B, KI21A, PPIE, PCM1, GALK1, MRP5, SE1L1, LIMD1, TCF20, SUN2, AFF4, UBQL2, S30BP, NRBP, SIX4, TASOR, GMEB2, PARP4, NUP50, ZHX1, YETS2, HECD1, SCAF8, SRRM2, SCML2, S22AL, NCOR2, DEMA, POLH, R3HD2, ZN281, FBX7, RPGF2, IRS2, HYOU1, PRC2C, NCOR2, GMEB1, S23IP, SRPK3, SLFN1, VNN1, KLK4, SE1L1, RGS6, E41L1
Species: Homo sapiens, Mus musculus
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Zaro BW, Batt AR, Chuh KN, Navarro MX, Pratt MR. The Small Molecule 2-Azido-2-deoxy-glucose Is a Metabolic Chemical Reporter of O-GlcNAc Modifications in Mammalian Cells, Revealing an Unexpected Promiscuity of O-GlcNAc Transferase. ACS chemical biology 2017 12(3) 28135057
Abstract:
Glycans can be directly labeled using unnatural monosaccharide analogs, termed metabolic chemical reporters (MCRs). These compounds enable the secondary visualization and identification of glycoproteins by taking advantage of bioorthogonal reactions. Most widely used MCRs have azides or alkynes at the 2-N-acetyl position but are not selective for one class of glycoprotein over others. To address this limitation, we are exploring additional MCRs that have bioorthogonal functionality at other positions. Here, we report the characterization of 2-azido-2-deoxy-glucose (2AzGlc). We find that 2AzGlc selectively labels intracellular O-GlcNAc modifications, which further supports a somewhat unexpected, structural flexibility in this pathway. In contrast to the endogenous modification N-acetyl-glucosamine (GlcNAc), we find that 2AzGlc is not dynamically removed from protein substrates and that treatment with higher concentrations of per-acetylated 2AzGlc is toxic to cells. Finally, we demonstrate that this toxicity is an inherent property of the small-molecule, as removal of the 6-acetyl-group renders the corresponding reporter nontoxic but still results in protein labeling.
O-GlcNAc proteins:
A2A5R8, A2A6U3, A2AF81, A2AG39, A2AIW9, A2AJ72, A2AJI1, A2AKV2, A2AL12, A2AMW0, A2AUR3, LAS1L, TRM1L, A5A4Y9, A6PWC3, B0QZF8, B1AU76, UPP, B7ZC19, B7ZP47, B8JJC1, D3YWF6, D3YWK1, D3YWS3, D3YYP4, E9PX53, E9Q066, I2BP2, E9Q4Q2, E9Q5L7, E9Q7W0, E9QP59, F8WGW3, G3UX26, G3UYZ0, G3UZ44, G3X972, H3BKW0, H7BWX9, GTPB1, AIP, ATOX1, HDAC1, GSH0, DHX15, IKBE, AKAP2, SLK, IMPCT, IF6, ACOT1, NMT1, DHB12, SRPK1, ZN326, KLC1, RPP30, IDHC, CASP8, GCR, TYSY, RIR1, S10AA, LEG1, G3P, TPIS, PRDX3, CBX3, TISD, CATA, IMDH2, NFKB1, MAP4, CEBPB, CDK4, FKBP4, HMGB2, KAP3, MP2K1, RANG, PTN11, FBRL, PTN12, FMR1, HMGCL, DYN1, CAP1, STAT1, STAT3, PURA, ALD2, SIPA1, PURA2, GSHR, FOSL2, FOSL1, GSTM5, PCY1A, VATA, HDGF, UBP10, RHOX5, HMGA2, CCHL, NUB1, FAF1, ZNRD2, TB182, PCBP1, ARL1, PFD3, TCTP, HMGB1, DYL1, UB2L3, HDAC2, ELAV1, 4EBP2, PYRG1, TCPB, SPTC2, PSME2, BOP1, WBP2, XDH, HMMR, E2AK2, CO6A1, FABP5, LARP7, CNN2, PP4R2, RM10, Q3TFP0, GUAA, FUBP2, TRADD, CTU2, Q3U4W8, SNX27, BABA1, EDC4, COBL1, SKAP2, ARH40, CSTOS, LRRF1, ZMAT1, Q45VK5, JIP4, MDC1, Q5SUW3, SRC8, SAMH1, KHDR1, SPB6, CAPR1, PAPS1, TS101, PA1B2, FNTA, IGBP1, FSCN1, FXR1, CBX5, RAI1, MELK, FOXC2, DBNL, CYTB, NDRG1, RALY, GPDM, RAB3I, F120A, NOP58, Q6DFZ1, TPM4, Q6NXL1, Q6NZD2, TNPO3, SMHD1, UGGG1, UBXN7, TXLNA, DC1L2, KI18B, JUPI2, LARP1, CAND2, ACAP2, HNRPQ, SPAG7, ATX2L, MAP6, ELP1, PJA2, PGRC2, KCMF1, Q80VB6, FA98B, WDTC1, CPPED, LPP, PEF1, IF4B, ATG4B, FTO, Q8BH80, PRUN1, AHSA1, RCC2, NCEH1, LSS, FBLN3, PPR18, SRRM2, MSRB3, PPME1, RL1D1, TBCD4, NHLC2, MAP1S, TLK1, CND2, RAE1L, SEP10, ZFP57, UBA6, UBA3, STON1, PPM1F, GNL3, PUR1, HMCS1, Q8K0C7, PDXK, ANGE2, LRC41, SDE2, DNM1L, ANLN, MATR3, CBR3, MEPCE, ERF3A, DC1L1, SPART, TDIF2, HEXI1, SNP47, UBP15, MAVS, UBXN4, ACSF2, MICU1, ZNG1, BACH, ISOC1, IPYR2, CSDE1, PIP30, GCSH, Q91X76, DUS3L, BAG2, KCC1A, TTC1, HNRLL, RIN1, PP6R3, MARC2, DBR1, ATAD3, PSIP1, NXF1, NONO, PLST, RRAGC, VMA5A, TARA, DDAH2, TADA1, GRPE1, ABD12, NU155, OGFR, NPM3, GLOD4, COPRS, DPOE4, MIEN1, TRAP1, VATG1, CHSP1, OCAD1, RANB3, MFR1L, NDUF7, TBC15, PPIL4, MPPB, CYBP, ZCHC8, CD37L, MMS19, ARPIN, HNRPM, NXP20, SPF27, TOE1, Q9D4G5, ATAD1, CF226, IPYR, ORN, CNN3, KAP0, PLIN3, AKAP8, EIF3F, IFG15, LIMA1, NEK7, RTN3, STK3, NUP50, SYSM, HSPB8, BAG3, CUL3, RABX5, CAF1A, DREB, TOM40, DNJC7, NFU1, FBX6, NUBP1, DEST, TEBP, ACOT9, NFKB2, KAD2, SKP1, PDC6I, VAPA, CARM1, RAD9A, IF2G, SAE2, TRIP6, MBD2, HNRPF
Species: Mus musculus
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