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7 protocols using pugnac

1

Transcriptional Regulation Assays

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OSMI-1 (Sigma, 50 μM), 6-Ac-CAS (GlycoSyn, 10 μM), PUGNAc (Toronto Research Chemicals, 10 μM) were used when indicated. The Myc-hOGT plasmid was provided by Dr. Xiaochun Yu at the University of Michigan (Chen et al., 2013 (link)). Ngn3-luc was generated by inserting a ~4.1 kb promoter of the mouse Ngn3 gene into the pGL3-basic vector. IRE-luc was generated by inserting the −1985 to −280 bp upstream of the mouse Irs2 gene that contains two insulin-response elements (IREs) into the pGL3-basic vector. pCMV6-mNgn3-Myc-DDK (#MR212139) was purchased from Origene. pCMV-FOXO1 (#12148) was purchased from Addgene. pCMV-FOXO-4A was generated with the QuikChange XL II Site-Directed Mutagenesis Kit (Agilent). HepG2 and Caco-2 cells were transfected with expression plasmids, luciferase reporters, and β-galactosidase or Renilla-luciferase using Lipofectamine 3000 (Invitrogen) or FuGENE HD (Promega). Cells were lysed and luciferase and β-galactosidase enzyme activities were measured using kits from Promega. Relative luciferase activity was determined by normalizing to β-galactosidase or Renilla-luc activity (Ruan et al., 2012 (link); Wang et al., 2018 (link)).
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2

Detecting O-GlcNAc Modifications by Western Blot

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Cells were lysed in cell lysis buffer for Western blot and IP (P0013, Beyotime Biotechnology, Jiangsu, People’s Republic of China) containing a protease inhibitor cocktail (Hoffman-La Roche Ltd., Basel, Switzerland) and 5 μM PUGNAc (an OGA inhibitor; Toronto Research Chemicals Inc., Toronto, Canada). Protein samples (50 μg) were separated by 12% sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and transferred to Immobilon-P membranes (EMD Millipore, Billerica, MA, USA). Antibodies to O-GlcNAc (RL2, Affinity Bio-Reagents, Golden, CO, USA; CTD110.6, Abcam plc, Cambridge, UK), OGT (F-12; Santa Cruz, CA, USA), Akt1 (Cell Signaling Technology, Beverly, MA, USA), phospho-Akt1 (Ser473, Cell Signaling Technology), and GAPDH (Santa Cruz, CA, USA) were used for detection by ECL detection reagent (GE Healthcare UK Ltd, Little Chalfont, UK).
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3

Cloning and Mutational Analysis of Human OGT

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The full-length cDNA of human OGT was cloned into the pEGFP-C1 vector. Internal deletion mutants and the enzyme-dead mutant (G598S) of OGT were generated using the QuickChange site-directed mutagenesis kit (Stratagene). Deletion mutants of OGT were constructed as described previously (37 (link)).
Antibodies used in this study include the following: anti-OGT antibody (Novaus), anti-γH2AX (Upstate Biotechnology, monoclonal and polyclonal), anti-O-GlcNAc (RL2 monoclonal [Abcam] and CTD110.6 monoclonal [Covance]), anti-FLAG (Sigma), anti-Myc (Sigma), anti-Actin (Sigma), anti-Mdc1 (Sigma), anti-PAR (Genetex, monoclonal), anti-Ku80 (Cell Signaling Technology), anti-Chk1 (Cell Signaling Technology), anti-phospho-Chk1 (Ser345,Cell Signaling Technology) and anti-phospho-SQTQ (Cell Signaling Technology). siRNA sequences were generated to target human OGT (5′-GCACATAGCAATCTGGCTTCC-3′ or 5′-CCAAACTTTCTGGATGCTTAT-3′).
The OGT inhibitor (ST045849) was purchased from TimTec and the O-GlcNAcase (OGA) inhibitor (PUGNAc) was purchased from Toronto Research Chemicals. The ATM inhibitor KU-55933 was purchased from Calbiochem. For cell treatment, a final concentration of 2 μM KU-55933 was added to the cell medium at the indicated timepoints.
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4

Lipofectamine-based Cell Transfection

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Lipofectamine™ was purchased from Invitrogen (Carlsbad, CA, USA), and PUGNAc was from Toronto Research Chemicals (North York, Ontario, Canada). Cell culture accessories were obtained from BD Biosciences (Franklin Lakes, NJ, USA). FBS and Dulbecco's modified Eagle's medium (DMEM) were purchased from Gibco‐BRL and BioWhiteker (Walkersville, MD, USA), and the other Chemicals not mentioned were purchased from Sigma (St. Louis, MO, USA).
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5

Analysis of O-GlcNAcylation and Signaling Proteins

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Cells were lysed for 15 min at ice bath using a lysis buffer (1% Triton X-100, 20 mM Tris pH 7.5, 1 mM MgCl2, 150 mM NaCl, 1 mM Na3VO4, 50 mM NaF, 1.5 mM EDTA, 10% glycerol, 20 mM β-glycerophosphate, 10 µg/ml aprotonin, 1 µM pepstatin A) containing 5 µM PUGNAc (an OGA inhibitor; Toronto Research Chemicals, Inc., North York, Canada). Protein samples (50 µg) were separated by 10% SDS-PAGE and transferred to polyvinylidene fluoride membranes (Merck KGaA, Darmstadt, Germany). The membrane was blocked with 5% non-fat dried milk in TBST for 1 h at room temperature and incubated overnight at 4°C with primary antibodies. Antibodies specific to O-GlcNAcylation (RL2; 1:1,000; Affinity BioReagents, Golden, CO, USA) and OGT (F-12; 1:500; Santa Cruz Biotechnology, Inc., Dallas, TX, USA) were used. RhoA (67B9; 1:1,000), MLC (3672; 1:1,000) and phosphorylated (p-)MLC (3671; 1:1,000) antibodies were obtained from Cell Signaling Technology, Inc. (Danvers, MA, USA). GAPDH antibody (sc-25778; 1:2,000) and horseradish peroxidase-linked goat anti-mouse (sc-2005; 1:2,000) and goat anti-rabbit (sc-2004; 1:2,000) IgG secondary antibodies were purchased from Santa Cruz Biotechnology, Inc. Development was carried out using an enhanced chemiluminescence western blotting detection reagent (GE Healthcare Life Sciences, Chalfont, UK).
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6

Transcriptional Regulation Assays

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OSMI-1 (Sigma, 50 μM), 6-Ac-CAS (GlycoSyn, 10 μM), PUGNAc (Toronto Research Chemicals, 10 μM) were used when indicated. The Myc-hOGT plasmid was provided by Dr. Xiaochun Yu at the University of Michigan (Chen et al., 2013 (link)). Ngn3-luc was generated by inserting a ~4.1 kb promoter of the mouse Ngn3 gene into the pGL3-basic vector. IRE-luc was generated by inserting the −1985 to −280 bp upstream of the mouse Irs2 gene that contains two insulin-response elements (IREs) into the pGL3-basic vector. pCMV6-mNgn3-Myc-DDK (#MR212139) was purchased from Origene. pCMV-FOXO1 (#12148) was purchased from Addgene. pCMV-FOXO-4A was generated with the QuikChange XL II Site-Directed Mutagenesis Kit (Agilent). HepG2 and Caco-2 cells were transfected with expression plasmids, luciferase reporters, and β-galactosidase or Renilla-luciferase using Lipofectamine 3000 (Invitrogen) or FuGENE HD (Promega). Cells were lysed and luciferase and β-galactosidase enzyme activities were measured using kits from Promega. Relative luciferase activity was determined by normalizing to β-galactosidase or Renilla-luc activity (Ruan et al., 2012 (link); Wang et al., 2018 (link)).
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7

Protein Extraction and Western Blot Analysis

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Cells were collected and lysed in 1 × RIPA lysis buffer (Cell Signaling, CST-9806) supplemented with [0.1% Sodium dodecyl sulfate (Sigma Aldrich, 436143), 0.1% Lauryl-beta-D-maltoside (Sigma-Aldrich, D4641), 0.5% Triton (ACROS, 21568–2500), 1 × PhosSTOP Phosphatase Inhibitor (ROCHE, 04906837001), 1 × cOmplete Mini Protease Inhibitor Cocktail (ROCHE, 11836153001), and 100 µM PugNAc (Toronto Research Chemicals, A157250)]. Lysed cells were incubated on ice for 30 min and centrifuged at 16,000×g at 4 ºC for 20 min. Protein concentration was determined using the Pierce™ BCA Protein Assay Kit (Thermo Fisher Scientific, 23228). Equal amounts of protein (30 µg) were mixed with reducing Laemmli loading buffer (BIORAD, 1610747), boiled and electrophoresed on hand poured acrylamide gels, then transferred to PVDF membranes (BIORAD, 1620177). Blocking was performed for 20–45 min with 5% dry milk (Nestle, 274200) in 1 × TBST and blotting performed with primary antibodies at 1:500–1000 dilutions overnight (16–18 h) at 4 ºC while rocking. Primary antibodies were detected with species specific HRP conjugated secondary antibodies. Specifically, Amersham ECL Prime Western Blotting Detection Reagent (Cytiva) for 2–3 min prior to image acquisition. Densitometry quantification of bands were performed as66 (link) using ImageJ.
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