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8 protocols using atr n 19

1

Molecular Mechanisms of Cellular Regulation

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All chemicals and solvents used in the present study were of highest grade available. InuA with a purity higher than 95% was prepared as reported previously [34 (link)]. The antibodies against human MDM2 (Ab-2), p21 (Ab-1), and p-H2AX (Ser139) were bought from EMD Chemicals (Gibbstown, NJ, USA). The antibodies against human p53 (DO-1), Cdk2 (M2), Cdk4 (H-22), Cdk6 (C-21), cyclin D1 (DCS-6), cyclin E (HE12), c-Myc (0.N.222), Bax (N-20), Bcl-2 (100), PARP (H-250), Chk1 (G-4), Chk2 (B-4), and ATR (N-19) were purchased from Santa Cruz Biotechnology (Santa Cruz, CA, USA). The antibodies against human p-Chk1 (Ser317), p-Chk2 (Thr68), and p-p53 (Ser15) were obtained from Cell Signaling Technology (Danvers, MA, USA). The anti-human NFAT1 (1/NFAT-1) antibody was sourced from BD Biosciences (San Jose, CA, USA) and the anti-human β-actin (AC-15) antibody was purchased from Sigma (St. Louis, MO, USA). The goat anti-mouse IgG (H+L) and goat anti-rabbit IgG (H+L) antibodies were bought from Bio-Rad (Hercules, CA, USA). The NFAT1 and MDM2 siRNA pool and control siRNA pool were obtained from Thermo Scientific (Rockford, IL, USA).
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2

Whole Cell Extract Immunoblotting

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Whole cell extracts were prepared by lysing cells in two volumes of Lysis Buffer (250 mM NaCl, 5 mM ethylenediaminetetraacetic acid (EDTA), 50 mM HEPES, 0.1% v/v NP40). A total of 60 μg of whole cell extract (WCE) was resolved on 4–12% NOVEX gels using MOPS buffer (Invitrogen). Protein was transferred to PVDF membrane (Invitrogen) and blotted for BCLAF1 (BTF 608A, Bethyl Labs); THRAP3 (A300–956A, Bethyl Labs), GAPDH (ab9485, Abcam), pATM (S1981) (ab79891 Abcam), ATM (2C1, Santa Cruz), pATR (S428) (2853, Cell Signaling), ATR (N-19, Santa Cruz), 53BP1 (NB100–34, Novus Biologicals), γH2AX (S139) (JBW301, Millipore), cyclin B1 (GNS1) (sc-245, Santa Cruz), pP53 (S15) (9284S, Cell Signaling), pKAP1 (S824) (A300–767A, Bethyl Labs), FANCD2 (FI17) (sc200–22, Santa Cruz), BRCA2 (H-300) (sc-8326, Santa Cruz), FANCL (B-11) (sc-137067, Santa Cruz), PALB2 (H-45) (sc-382436, Santa Cruz) and Rad51 (3C10) (sc-53428, Santa Cruz).
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3

Histone Modifications and DNA Damage Signaling

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The following antibodies were used: Histone H3 (ab1791, Abcam); H3K4me1 (07-436, Millipore); H3K4me2 (07-030, Millipore); H3K4me3 (ab8580, Abcam); H3K9me1 (ab9045, Abcam); H3K9me2 (ab1220, Abcam); H3K9me3 (ab8898, Abcam); SUV39H1#1 (07-958, Millipore); SUV39H1#2 (Active Motif); MRE11 (NB100-142, Novus Biologicals); NBS1 (NB100-143, Novus Biologicals); ATM (Ab-3, Calbiochem); ATR (N19, SantaCruz); phospho-γH2AX (05-636, Millipore), UPF1 (generous gift of Dr. Claus Azzalin)62 (link); α - phospho-(Ser/Thr) ATM/ATR substrate (6966, Cell Signaling).
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4

Immunoblotting for Telomere Regulatory Factors

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Immunoblotting was performed as described previously (Celli et al., 2006 (link); Kibe et al., 2010 (link)). The following primary antibodies were used: TRF1 (1449, de Lange lab); TRF2 (1254 or 1255, de Lange lab); Rif1 (1240, de Lange lab); TPP1 (ab104297, Abcam); 53BP1 (NB100–305, Novus Biological); ATR (N-19, Santa Cruz); CtIP (H-300, Santa Cruz); Exo1 (A302–640A, Bethyl Laboratories, Inc.); BLM (ab2179, Abcam); TopBP1 (ab2402, Abcam); mTOR (#2972, Cell Signaling Technology); γ-tubulin (GTU-88, Sigma-Aldrich); FLAG (M2, Sigma-Aldrich). The chemiluminescent signals were detected using ECL Western Blotting Detection Reagents (GE healthcare) and BioMax MR film or XAR film (Kodak) according to the manufacturer’s protocol.
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5

Reagents and Antibodies for Protein Analysis

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LinA was prepared as described in our previous study[48 ]. All chemicals and solvents used in the present study were of highest grade available. Fetal bovine serum (FBS) was obtained from Atlanta Biologicals (Lawrenceville, GA, USA). The penicillin/streptomycin preparation was bought from Corning (Manassas, VA, USA). The anti-human NFAT1 (1/NFAT-1) antibody was purchased from BD Biosciences (San Jose, CA, USA). The antibodies against human MDM2 (Ab-2), p21 (Ab-1), and p-H2AX (Ser139) were sourced from EMD Chemicals (Gibbstown, NJ, USA). The antibodies against human p53 (DO-1), Cdk2 (M2), Cdk4 (H-22), Cdk6 (C-21), cyclin D1 (DCS-6), cyclin E (HE12), c-Myc (0.N.222), Bax (N-20), Bcl-2 (100), PARP (H-250), Chk1 (G-4), Chk2 (B-4), and ATR (N-19) were obtained from Santa Cruz Biotechnology (Santa Cruz, CA, USA). The antibodies against human p-Chk1 (Ser317), p-Chk2 (Thr68), and p-p53 (Ser15 (link)) were purchased from Cell Signaling Technology (Danvers, MA, USA). The anti-human β-actin (AC-15) antibody was bought from Sigma (St. Louis, MO, USA) and the goat anti-mouse IgG (H+L) and goat anti-rabbit IgG (H+L) antibodies were obtained from Bio-Rad (Hercules, CA, USA).
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6

Quantitative Protein Analysis by SDS-PAGE and Western Blot

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Total protein was extracted from exponentially growing cells at passage 8–10 and 40 g/mL were resolved by SDS-PAGE using a 4–15% gradient gel (Bio-Rad Laboratories). After transfer and blocking overnight at 4 °C in Odyssey Blocking Buffer (Li-Cor, Lincoln, NE, USA) proteins were detected by primary antibodies against BRCA1 [2A-9] (1:500, kindly provided by Stephen Smith, Leibnitz Institute, Jena, Germany), ATR [N-19] (Santa Cruz, St. Cruz, CA, USA, 1:1000), CHK1 [2G1D5] (Cell Signaling, Danvers, MA, USA, 1:750), RAD51 [14B4] (1:2.000, GeneTex, Irvine, CA, USA), MRE11A [12D7] (Abcam, Cambridge, UK, 1:500), pCHK1 [Ser296] (Cell Signaling, 1:1000), -actin [AC-74] (1:50.000, Sigma, St. Louis, MO, USA). Primary antibodies were detected with IRDYE 680 conjugated anti-mouse IgG, IRDYE 800 conjugated anti-rabbit IgG (Li-Cor, 1:7500), IRDYE 680 conjugated anti-rabbit IgG (Licor, 1:7.500 or 15.000) or IRDYE 800 conjugated anti-mouse IgG (Li-Cor 1:7.500 or 15.000). Quantitative and qualitative analysis was done by using Li-Cor Odyssey (Li-Cor, Lincoln, NE, USA).
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7

DNA Damage Response Protein Assay

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ATM (Cell Signaling 2873s), ATM S1981 (Cell Signaling 4526L), ATR (N19) (Santa Cruz sc-1807), BRCA2 [15 (link)], DNA-PKcs S2056 (Abcam ab18192), gamma-H2AX [16 (link)], 53BP1 [17 (link)], RAD51 [15 (link)], Actin (Sigma A5441), GAPDH (Chemicon MAB374), H3 (Cell Signaling 9715s), CHK1 (Santa Cruz sc-8048), and mouse anti-BrdU (BD Biosciences 347-580 B44) were used at 1:500 dilution. All secondary antibodies were purchased from Jackson Immuno Research Laboratories and were used at 1:3000 dilution.
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8

Immunoblotting Protein Detection Protocol

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Immunoblotting was performed as described previously (Celli et al., 2006 (link)). The following primary antibodies were used: TRF1 (1449), TRF2 (1255), MYC (9E10, Cell Signaling), ATR (N-19, Santa Cruz), LIG3 (611876; BD Transduction), and γ-tubulin (GTU-88, Sigma-Aldrich). The chemiluminescent signals were detected using enhanced chemiluminescence western blotting detection reagents (GE Healthcare) and BioMax MR film or XAR film (Kodak) according to the manufacturer’s protocol.
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