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8 protocols using myc 4a6

1

Protein Turnover Dynamics Analysis

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The turnover of ΔssCPY-GFP and Hmg2-myc was assessed in cells by inhibiting protein synthesis with cycloheximide. Cells were collected at the indicated time points and ΔssCPY-GFP and Hmg2-myc levels analyzed by immunoblotting and quantified by densitometry. Values shown are percentages relative to zero time points from three independent biological repeats. Protein extracts were electrophoresed under reducing conditions on NuPAGE minigels (Thermo Fisher Scientific) and electroblotted onto polyvinylidene fluoride membrane (GE Healthcare). Primary antibodies used were rabbit α-Sup35 (Ness et al., 2002 (link)), ubiquitin (sc-8017; Santa Cruz Biotechnology, Inc.), Ydj1 (ab74442; Abcam), Sis1 (COP-080051; Operon Biotechnologies), Ssa1 (ADI-SPA-822; Enzo Life Sciences), GFP (A6465, Invitrogen), Pgk1 (459250; Thermo Fisher Scientific), Hsp104 (ab2924; Abcam), rabbit α-Sse1 (Chiabudini et al., 2012 (link)), and Myc 4A6 (05–724; EMD Millipore).
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2

Immunofluorescence Staining of Protein Complexes

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After fixation, beads were washed in AbDil (20 mM Tris-HCl, pH 7.4, 150 mM NaCl with 0.1% Triton X-100, and 2% bovine serum albumin), pipetted onto poly(l-lysine)-coated coverslips and allowed to adhere for ≥30 min. Coverslips were stained in primary antibody diluted in AbDil for ≥20 min and then washed in AbDil. Primary antibodies used were 2 µg/ml FLAG (F7425 [rabbit] and F1804 [mouse], both obtained from Sigma-Aldrich), 0.25 µg/ml Myc (4A6; EMD Millipore) 1 µg/ml xCENP-C (rabbit, raised and purified against xCENP-C207–296; Milks et al., 2009 (link)), and 1.5 µg/ml xM18BP1 (rabbit, raised against GST-xM18BP1-2 amino acids 161–415 and purified against xM18BP1-1161–375; Moree et al., 2011 (link)). Coverslips were then stained in secondary antibodies diluted in AbDil for ≥20 min, and then washed in AbDil. Secondary antibodies used were Alexa Fluor 488–conjugated donkey anti–rabbit (Jackson ImmunoResearch Laboratories, Inc.), Alexa Fluor 647–conjugated donkey anti–rabbit (Jackson ImmunoResearch Laboratories, Inc.), and Alexa Fluor 647–conjugated goat anti–mouse (Life Technologies) all at 2 µg/ml. Coverslips were washed in PBST and PBS, gently blotted with filter paper, and mounted in 90% glycerol, 10 mM Tris, pH 8.8, 0.5% p-phenylenediamine. Coverslips were sealed to a slide with clear nail polish.
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3

Yeast Cell Lysates and Western Blotting

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S. cerevisiae whole cell lysates and western blotting analysis were performed as described.28 (link) Antibodies including catalog number and manufacturer used in this study were: MYC (4A6, Millipore), HA (3F10, Roche), Clb2 (sc-9071, Santa Cruz), PCNA (ab70472, Abcam), Rnr3 (AS09574, Agrisera), tubulin-Rnr4 (YL1/2, Sigma), Histone H3 (ab46765, Abcam) and Sic1 (previously described45 (link)). In order to detect PCNA more efficiently with the anti-PCNA antibody (ab70472, Abcam), the membrane was incubated in a mild stripping buffer (0.2 M glycine pH 2.2, 0.1% SDS, 1% Tween 20) prior to blocking.
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4

Western Blot Protein Detection

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IP samples were resolved by SDS–PAGE, electroblotted onto nitrocellulose membrane and probed using the relevant primary antibody (Myc 4A6, Millipore 05–724; FLAG, Sigma F3165). Bound antibody was visualized using WesternSure Chemiluminescent Reagents (LI-COR).
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5

Histone Modifications Profiling by ChIP

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Mouse monoclonal antibodies against the following histone modifications were used: H3K9me2 (m5.1.1) (36 (link)), H3K36me2, H3K36me3, H3K9Ac and H3K14Ac (37 (link),38 (link)). Mouse monoclonal antibodies against epitope tags, i.e. Myc (4A6, Millipore) and FLAG (M2, Sigma), were used in the ChIP assay and immunoblotting. Mouse monoclonal antibody against Pol2 CTD phosphorylated at Ser5 (4H8, Abcam), rabbit polyclonal antibody against the N-terminal half of Rpb1 (39 (link)) and rabbit polyclonal antibody against histone H3 C-terminal (Millipore) were used for immunoblotting.
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6

Yeast Cell Lysates and Western Blotting

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S. cerevisiae whole cell lysates and western blotting analysis were performed as described.28 (link) Antibodies including catalog number and manufacturer used in this study were: MYC (4A6, Millipore), HA (3F10, Roche), Clb2 (sc-9071, Santa Cruz), PCNA (ab70472, Abcam), Rnr3 (AS09574, Agrisera), tubulin-Rnr4 (YL1/2, Sigma), Histone H3 (ab46765, Abcam) and Sic1 (previously described45 (link)). In order to detect PCNA more efficiently with the anti-PCNA antibody (ab70472, Abcam), the membrane was incubated in a mild stripping buffer (0.2 M glycine pH 2.2, 0.1% SDS, 1% Tween 20) prior to blocking.
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7

Redox state assessment of Tsa1 and Bcy1

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The redox state of Tsa1 or Bcy1 was assessed as described previously (79 (link)) except the thiol-reactive probe 4-acetamido-4’maleimidyldystilbene-2,2’ disulfonic acid (AMS) was substituted for methoxypolyethylene glycol maleimide ((mPEG-MAL)-5000, Sigma). Protein extracts were electrophoresed on reducing NuPAGE protein minigels (Life Technologies) and electroblotted onto nitrocellulose membranes. Bound antibody was visualized using WesternSure Chemiluminescent Reagents (LI-COR). For nonreducing western blot analysis, proteins were extracted in the presence of N-ethylmaleimide (NEM) to prevent any nonspecific thiol oxidation during sample preparation. Primary antibodies used were Tsa1 (70 (link)), FLAG (F3165, Sigma), Myc 4A6 (05-724, Millipore), Prx-SO2/3 (ab16830, Abcam), phospho-PKA (100G7E, Cell Signaling Technology), and Pgk1 (sc-130335, Santa Cruz).
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8

Antibodies for Chromatin Immunoprecipitation

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Rabbit polyclonal antibodies against Cnp1 (28 (link)) and histone H3 (ab1791) were obtained from Abcam. Mouse monoclonal antibodies against H3K9me (29 (link)), H3K14ac (7G8) and Pol2 CTD (4H8) were obtained from Millipore. Mouse monoclonal antibodies against epitope tags, Myc (4A6/Millipore) and FLAG (M2/Sigma) were used for ChIP assays and immunoblotting.
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