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7 protocols using pkap1

1

Protein Extraction and Western Blot Analysis

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The protein extraction from cell lysate or tissue lysate was prepared in urea lysis buffer (8 M urea, 1% SDS, 100 mM NaCl, 10 mM Tris (pH 7.5) and incubated for 30 min on ice after which the samples were sonicated for 10 seconds. Western blotting was performed as per the standard protocol and some of the antibodies used for immunoblotting17 (link). The following are additional antibodies used in this study: Cell Signaling antibodies: PARP (#9542), pAKTS473 (#4060), AKT (#9272), pPdk1S241 (#3061), Pdk1(#3062) Chk1 (2G1D5) (#2360), p-GSK-3β(Ser9) (#9336), GSK-3β (#9315), p-Histone H3 (#9706) (1:1000 dilution); Millipore antibody: Chk2 (1:500 dilution) (Clone 7) (05-649), γ-H2ax (1:1000 dilution) S139 (05-636); BD Pharmingen antibody: β-actin (1:2000 dilution) (612656); Bethyl antibody: pKap1(S824) (1:1000 dilution) (A300-767A). Immunoprecipitation was performed as per our previous publication45 (link). Immunodetections were performed using Bubr1 (ab4637), Mad2 (CST4636S) and CDC20 (CST14866A).
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2

Southern Blot Analysis of Lymphoid Tissues

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For Southern blot analyses, genomic DNA from the spleen, tumor and corresponding kidneys was digested with EcoRI (for JH4, c-Myc, constant region of TCRδ probe) KpnI (for 3′ ATM CKO probe), or HindIII (for the IgK probe) (22 (link)–24 ). To avoid cross-reactivity with the EμCyclinD1 transgene that includes a fragment from JH4 to μ enhancer, we generated a new JH4 probe by PCR amplification with the following primers: 5′-TGGTGACAATTTCAGGGTCA-3′ and 5′-TTGAGACCGAGGCTAGATGC-3′. For Western blots, stimulated splenic B or T-cells were probed with antibodies against ATM (1:2000, MAT3, Sigma, St. Louis, MO), pKap1 (1:2000, Bethyl, Montgomery, TX), Kap1/TIF1β (1:1000, Cell Signaling, Danvers, MA), β-Actin (1:10,000, A5316, Sigma) and CyclinD1 (1:1000, Abcam).
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3

Antibody-based Western Blot Analysis Protocol

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Antibodies used for Western blot analysis included the following: anti-C1orf55/SDE2 (epitope: a.a. 318–410; Sigma-Aldrich), anti-GFP (JL-8, Clontech), anti-HA (6E2, Cell Signaling), anti-pCHK1 (S317, Cell Signaling), anti-Actin (Cell Signaling), anti-CDT1 (Cell Signaling), anti-Flag (M2, Sigma-Aldrich), anti-Tubulin (Sigma-Aldrich), Cyclin E (H-12, Santa Cruz), anti-PCNA (PC-10, Santa Cruz), anti-Vinculin (H-300, Santa Cruz), anti-GST (B-14, Santa Cruz), Cyclin A (H-432, Santa Cruz), anti-γH2AX (JBW301, Millipore), anti-CDT2 (Bethyl), anti-pRPA (S33, Bethyl), pKAP-1 (S824, Bethyl), anti-ORC2 (BD Pharmingen), and anti-MUS81 (MTA30 2G10/3, Abcam). Mitomycin C, camptothecin, hydroxyurea, cycloheximide, aphidicolin, and Z-Leu-Leu-Leu-al (MG132) were purchased from Sigma-Aldrich. Rucaparib (AG-014699) was purchased from Selleckchem. MLN4924, ubiquitin vinyl sulfone, and ubiquitin aldehyde were purchased from Boston Biochem. Drugs were used at the concentrations indicated in the figure legends.
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4

Probing Signaling Cascades in NSCs

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For Western Blots (WB), NSCs were extracted in RIPA lysis buffer (NEB) supplemented with protease inhibitors (Sigma). For immunoprecipitation (IP) cells were lysed in IP buffer (20mM sodium phosphate buffer, 1 mM EDTA, 0.2% NP40, 150 mM NaCl supplemented with Na-orthovanadate, PMSF, NaF and protease inhibitor mixture [Sigma]). After sonication and centrifugation, supernatant was incubated overnight at 4°C with Pdgfra antibody, followed by 2-hr incubation with Dynabeads M-280 (Invitrogen), washed with IP buffer (0 mM NaCl, 150 mM NaCl and 1 M NaCl) and eluted in Laemmli sample buffer. All primary antibodies were used at 1:1000 dilution and secondary antibodies at 1:10000. The following antibodies were used: p53, Pdgfra, p-Pdgfra, p-Chk2, p-Akt, Akt (all Cell Signaling); Myc-9E10 (CRUK); Smc1 (Abcam); p-Smc1, Chk2, Tubulin (all Merck); p-Kap1, Kap1 (both Bethyl Labs); Atm (Santa Cruz), p-Atm (Epitomics), p-p53, Actin, GAPDH, HRP-conjugated goat anti-mouse/rabbit IgG (all Sigma).
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5

Western Blot Analysis of DNA Damage Signaling

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Cells lysates resuspended in Laemmli buffer (100 mM Tris-HCl, pH 6.8, 200 mM dithiothreitol, 3% SDS, 20% glycerol and 0.05% bromophenol blue) were separated on a Mini-PROTEAN TGX Stain-Free Precast Gel (Bio-Rad), transferred to a nitrocellulose membrane and incubated with the following primary antibodies: p-KAP1 (1:1,000 dilution, A300-767A, Bethyl); CHK2 (1:250 dilution; 611570, BD Transduction Laboratories); γH2AX (1:1,000 dilution, 05–636, Millipore); ZSCAN4C (1:1,000 dilution, AB4340, Millipore Sigma); and tubulin (1:5,000 dilution, T5168, Millipore Sigma). Protein signals were visualized on a ChemiDoc MP Imaging System (Bio-Rad) using the following secondary antibodies: mouse DyLight-680 or rabbit DyLight-800 antibodies (1:5,000 dilution, Invitrogen). Imaging processing to remove non-relevant portions was performed using Adobe Photoshop CC 2020. Uncropped and unprocessed images are provided in the Source Data for Figs. 3g, 4c, Extended Data Figs. 2f, g, 6e.
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6

DNA Damage Response Protein Analysis

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Primary antibodies: RAD51 (Merk, Ab-1, PC130, 1:1000), RAD52 (Thermo Fisher, PA5-65036, 1:500), XAB2 (abcam, ab129487, 1:1000), CtIP (Active Motif, 61141, 1:500), ATM (abcam, ab32420 (Y170), 1:1000), P-ATM (abcam, ab81292 (pS1981), 1:50000), P-KAP1 (Bethyl, IHC-00073 (pS824) 1:200).
Secondary antibodies: HRP rabbit (Jackson Laboratory, Cat. No. 111-035-003, 1:50 000), HRP mouse (Amersham/Sigma, Cat. No. GENA931-1ML, 1:10 000), HRP mouse (Santa Cruz, sc-516102, 1:10 000).
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7

Quantitative Western Blot Analysis

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Western blotting was performed as previously described (Zong et al, 2015 (link)). Briefly, cells were washed in PBS and lysed in an extraction buffer containing 50 mM Tris-HCl (pH 7.5), 200 mM NaCl, 5% Tween-20, 2% Igepal, 2 mM PMSF, 2.5 mM b-glycerophosphate (all from Sigma) and supplemented with protease and phosphatase inhibitor tablets (both Roche Diagnostics). Equal amounts of protein were loaded into precast 4–12% Bis-Tris mini-gels (Invitrogen) and resolved by SDS-PAGE. Thereafter, proteins were transferred onto nitrocellulose membranes, blocked in a TBS-based blocking agent (LiCor Biosciences) and incubated with the corresponding primary antibodies recognizing the following proteins: WRN (1:1000, Novus), FLAG (1:1000, Sigma), pKAP1 (S824, 1:1000, Bethyl), pATR (T1989, 1:500, Cell Signaling), pCHK1 (S345, 1:500, Cell Signaling), pCHK1 (S317, 1:500, Novus), pCHK1 (S296, 1:1000, gift of Dr. Lee Jung-Min), CHK1 (1:1000, Cell Signaling), pRPA2 (S33, 1:1000, Bethyl), RPA2 (1:2000, Cell Signaling), pCHK2 (T68, 1:1000, Cell Signaling), CHK2 (1:1000, Cell Signaling), β-actin (1:5000, Sigma) and Tubulin (1:5000, Sigma). Fluorescently labeled secondary antibodies were used at a dilution of 1:10,000 (Li-Cor Biosciences). Visualization and quantification of protein bands was achieved by fluorescence imaging using a Li-Cor Odyssey CLx imaging system (Li-Cor Biosciences).
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