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4 protocols using flag m2 conjugated agarose beads

1

Quantifying PITX2-NRF2/YAP1 Interactions

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Transfected 293T cells were harvested and lysed in lysis buffer (50 mM Tris-HCl, pH 7.5, 150 mM NaCl, 1% Nonidet P-40, 0.5% sodium deoxycholate and 1% protease inhibitor cocktails; Sigma, St. Louis, MO, USA) and incubated on ice for 5 min with periodic agitation. Cell lysates were centrifuged, and the supernatant was incubated with antibodies of interest and Protein G Plus/Protein A agarose beads (Sigma, St. Louis, MO, USA) or Flag M2-conjugated agarose beads (Sigma, St. Louis, MO, USA) at 4 °C overnight. The beads were washed six times with cell lysis buffer, and the precipitated proteins were further analyzed by western analysis.
To quantify the interaction between WT/mutant PITX2 and NRF2/ YAP1, ImageJ was used to calculate the intensity of the targeted protein. The intensity of IP bands/ input bands was calculated to normalize the total protein content. The relative binding capacity was quantified by the normalized IP-HA intensity/normalized IP-Flag intensity. At least three independent co-IP experiments were conducted, and one typical blot is presented.
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2

Comprehensive Immunoblotting Protocol for Cell Signaling

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UBQLN1 #14526, UBQLN2 #85509, Cyclin D1 #2978, Cyclin D3 #2936, Cyclin A2 #4656, Cyclin E1 #4129, Cyclin E2 #4132, Cyclin H #2927, Cyclin B1 #4138, CDK2 #2546, CDK4 #2906, CDK6 #3136, GAPDH #5174, c-MYC #9402, p-MYC #13748, MYCBP #517020, VDAC # 4866, CREB #9197, Cdc42 #2462, E-cadherin #3195, N-cadherin #13116, Snail #3879, Slug #9585, Zeb1 #3396, β-catenin #8480, Claudin1 #4933, GFP #2956, (Cell Signaling Technologies Inc. Danvers, MA, USA); Tubulin #B512, FLAG M2 conjugated agarose beads, FLAG poly-clonal #F7425, FLAG Peptide #F-3290 (Sigma-Aldrich, Inc. St. Louis, MO, USA); UBQLN3#376548, UBQLN4 #136145, β-actin #517582 (Santa Cruz Biotechnology, Inc. Dallas, TX, USA); Alexa Fluor 488 goat anti-rabbit IgG #A11034 (Molecular Probes, Invitrogen detection technologies, Eugene, OR, USA); Alexa Fluor 568 Phalloidin #A12380 (Life technologies, Eugene, OR, USA). Ubqln polyclonal was made by inoculating rabbits with a peptide specific to Ubqln1 (Yenzym Antibodies LLC, Brisbane, CA, USA).
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3

Immunoprecipitation and Immunoblotting Protocol

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Cells were harvested and lysed using sonication with diagenode Bioruptor UCD-200 in cell lysis buffer (50 mM Tris-HCl, pH 7.5, 150 mM NaCl, 1% Nonidet P-40, 0.5% sodium deoxycholate and 1% protease inhibitor cocktails, Sigma-Aldrich). Cell lysates were centrifuged and the supernatant was incubated with indicated antibodies and Protein G Plus/Protein A Agarose beads (Calbiochem) or FLAG M2-conjugated agarose beads (Sigma Aldrich) at 4°C overnight. The beads were washed six times with cell lysis buffer and the precipitated proteins were further analyzed. For western blotting, equal amounts of protein (80–100 micrograms) from cell lysates were denatured in sample buffer (Thermo Fisher Scientific), subjected to SDS-polyacrylamide gel electrophoresis (Bio-Rad) and transferred to nitrocellulose membranes (Thermo Fisher Scientific). The membranes were blocked in 1× TBST with 5% milk, immunoblotted with indicated primary antibodies at 4°C overnight, followed by incubation at room temperature for 1 hour with horseradish peroxidase-conjugated secondary antibodies. Blots were visualized by SuperSignal West Pico Luminol Enhancer Solution (Thermo Fisher Scientific). BET inhibitors (JQ1 and iBET762) or DMSO as control were added directly to cell lysate (2 μM) during incubation with beads.
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4

Co-Immunoprecipitation and Western Blotting

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Cells were harvested and lysed by sonication with a Diagenode Bioruptor UCD-200 in cell lysis buffer (50 mM Tris-HCl, pH 7.5, 150 mM NaCl, 1% Nonidet P-40, 0.5% sodium deoxycholate, and 1% protease inhibitor cocktails; Sigma-Aldrich) for co-immunoprecipitation analysis (Co-IP). Cell lysates were centrifuged, and the supernatant was incubated with the appropriate antibodies and Protein G Plus/Protein A agarose beads (Calbiochem) or FLAG M2-conjugated agarose beads (Sigma-Aldrich) at 4°C overnight. The beads were washed six times with cell lysis buffer, and the precipitated proteins were further analyzed. For western blotting, equal amounts of protein (80–100 µg) from cell lysates were denatured in sample buffer (Thermo Fisher Scientific), subjected to sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE; Bio-Rad), and transferred to nitrocellulose membranes (Thermo Fisher Scientific). The membranes were blocked in 1 × tris buffered saline Tween (TBST) with 5% milk and immunoblotted with the appropriate primary antibodies at 4°C overnight, followed by incubation at room temperature for 1 h with horseradish peroxidase-conjugated secondary antibodies. Bands were developed using an enhanced chemiluminescence (ECL) kit (Millipore, Billerica, MA, USA).
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