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12 protocols using anti eed

1

EZH2 Interactome Profiling

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DMSO or inhibitor treated cells were washed twice with 1X PBS and whole cell lysates were prepared using lysis buffer (20 mM HEPES, pH 7.8, 150 mM NaCl, 10 mM EDTA, 2 mM EGTA, and 2 mM dithiothreitol, and 0.1% Nonidet P–40). The cell lysates were mixed with Dynabeads conjugated with anti–EZH2 antibody (Cell Signaling) and rotated at 4 °C overnight before removal of the supernatant. The resulting samples were analyzed by Western blot analysis using anti–SUZ12 (Cell Signaling) and anti–EED (Milipore) antibodies.
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2

Comprehensive Protein Expression Analysis

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Cells were lysed in RIPA lysis buffer (50 mM Tris-HCL [pH 8], 150 mM NaCl, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, protease inhibitors) for 30 min at 4°C. Protein extracts were resolved by SDS-PAGE and blotted to Nitrocellulose membranes and probed with the following antibodies: anti-beta Actin (Sigma-Aldrich, A5441), anti–EZH2 (AC22, Cell Signaling Technology, 3147S), anti-EZH2 (D2C9, Cell Signaling, 5246), anti-pT487 EZH2 (Abcam, ab109398), anti–SUZ12 (Cell Signaling Technology, 3737S), anti–EED (Millipore, 09-774), anti-EZH1 (Abcam, ab13665), anti-total H3 (Abcam, ab39763), anti-H3K27me3 (Cell Signaling Technologies, 9733), anti-V5 (Abcam, ab9116), anti-total CDK1 (Cell Signaling Technologies, 9112S), anti-pCDK1 (Cell Signaling Technologies, 9111S), anti-MRP1/ABCC1 (Santa Cruz, sc-18835), anti-Ubiquitin (Abcam, ab7780), anti-HOXB7 (Abcam, ab51237), anti-HOXA9 (Abcam, ab140631), anti-TRIM21 antibody (Abcam, ab91432), anti-HSP90 antibody (Abcam, ab13495) and anti-STIP1 antibody (Abcam, ab126724).
Densitometric analysis was performed using ImageJ software (NIH, Bethesda, MD).
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3

ChIP and Immunoblotting Protocol

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The following antibodies were used for Chromatin Immunoprecipitation (ChIP), RNA-binding protein Immunoprecipitation (RIP) or immunoblotting: anti-H3K27me3 (17–622, Millipore), anti-H3K9me3 (ab8898, Abcam), anti-EZH2 (07–689, Millipore), anti-SUZ12 (3737, Cell Signaling Technology), anti-EED (17–663, Millipore), anti-GAPDH (M20006, Abmart).
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4

Recombinant GST-EZH2 Fusion Proteins

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EZH2 fragments (1–173, 174–335, 336–554, 555–746) and EZH2-N (1–554) were amplified by PCR and subcloned into pGEX-4T-1 vector (GE Healthcare Life Sciences) to generate recombinant GST-EZH2 fusion proteins. Different regions of MALAT1 (M1-M6) were amplified from purified cDNA of C4-2 cells and subcloned into the backbone vector pcDNA3.1 (Life Technologies). Antibodies used are as follows: anti-EZH2 (XP, Cell Signaling Technology); anti-EED (Millipore); anti-DAB2IP (Abcam); anti-SUZ12 and anti-ERK2 (Santa Cruz Biotechnology); and anti-GST (GE Healthcare Life Sciences).
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5

Comprehensive Protein Expression Analysis

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Lysates were prepared in RIPA buffer [16 (link)], and western blotting was performed as described [17 (link)]. The following antibodies were used for western blot analysis: anti-Ezh2 (BD Biosciences #612666), anti-Suz12 (Cell Signaling 3737S), anti-Eed (Millipore 05–1320), anti-H3K27me1 (Millipore 07–448), anti-H3K27me2 (Millipore 07–452), anti-H3K27me3 (Millipore 07–449), anti-Histone 3 (Millipore 07–690), anti-β-actin (Sigma A5441), anti-Gapdh (Sigma G8795), anti-ERα (Millipore 07–690), anti-Ezh1 (Millipore 07–690), anti-PARP (Cell Signaling #9542), anti-p16 (Santa Cruz M-156), and anti-p19 (Rockland Immunochemicals #200-501-891). Secondary antibodies included HRP-conjugated anti-rabbit and anti-mouse (Southern Biotech), both 1:10,000.
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6

Chromatin Immunoprecipitation of HIV-1 Genome

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ChIP was performed as previously described (24 (link)), with the Pierce agarose ChIP kit (Thermo Scientific). For ChIP, anti-RNAP II (17-672 [Millipore] or sc-899 [Santa Cruz]), anti-EZH2 (17-662; Millipore), anti-EED (17-10034; Millipore), anti-SUZ12 (17-661; Millipore), anti-Jarid2 (AB192252; Abcam, Inc.), anti-histone H3 (AB1791; Abcam, Inc.), anti-histone H3K27me3 (AB6002; Abcam, Inc.), anti-EHMT2 (3356S; Cell Signaling), anti-SUV39H1 (8729S; Cell Signaling), anti-KDM1 (LSD1) (2139S; Cell Signaling), anti-trimethyl histone H3 (Lys9) (AB8898, Abcam, Inc.), and anti-dimethyl histone H3 (Lys9) (AB1220; Abcam, Inc.) antibodies were used. The percentage-of-input method was used to calculate the enrichment of proteins in specific regions of the HIV-1 genome.
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7

Comprehensive Chromatin Remodeling Antibody Panel

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The sources of the antibodies were anti-FLAG, anti-HDAC1 anti-HDAC2, anti-RbAp46/48, anti-Fibronectin, anti-Vimentin and anti-β-actin (Sigma–Aldrich); anti-DDB1, anti-MTA1, anti-SIN3A, anti-SAP180 and anti-SAP30 (Santa Cruz Biotechnology); anti-PRMT5, anti-ROC1, anti-LSD1, anti-DNMT3B, anti-HDAC5 and anti-MTA2 (Abcam); anti-EED, anti-MBD2/3 and anti-MTA3 (Millipore); anti-SUZ12 (Cell Signaling Technology); anti-WDR77 (also known as MEP50, Bethyl); anti-MTA2, anti-E-cadherin, anti-α-catenin, anti-γ-catenin, anti-N-cadherin and anti-EZH2 (BD Bioscience); anti-ING4 (Genetex), anti-SETD2 (Proteintech). Dynabeads Protein G was obtained from Invitrogen by Thermo Fisher Scientific, and protease inhibitor mixture cocktail was from Roche Applied Science. Glutathione-Sepharose 4B beads were from GE Healthcare Bio-Sciences. Short hairpin RNAs (shRNAs) were obtained from GenePharma Co Ltd (Shanghai, China).
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8

Epigenetic Complexes Profiling by Co-Immunoprecipitation

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Immunoprecipitation was performed using the Pierce™ Co-Immunoprecipitation Kit (#26149). Columns were prepared with 20–40 ug of antibody. Whole Protein lysate was incubated with antibody. Flow through was collected and column was washed and eluted. Antibodies used were: anti-EZH2 (Cell Signaling Technology), anti-SUZ12 (Cell Signaling Technology), anti-RbAP 46/48 (Cell Signaling Technology), anti-EED (Millipore), anti-HDAC2 (Cell Signaling Technology), anti-DNMT3L (Novus Biologicals). Experiments were performed at least three times.
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9

Comprehensive Protein Marker Analysis

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Anti-Flag (F-3165, 1:5000, Sigma), anti-HA (SC-7392, 1:2000, Santa Cruz Biotechnology), anti-MYC (AE010, 1:1000, Abclonal Technology), Anti-TUBULIN (SC-23948, 1:10000, Santa Cruz Biotechnology). Anti-Aggrecan (13880-1-AP,1:1000, Proteintech); Anti-MMP13 (18165-1-AP, 1:1000, Abcam); Anti-ADAMTS5 (PA5-14350, 1:1000, Thermo); Anti-ZMPSTE24(A-8858, IHC 1:50, ABclonal). Anti-H3K27me1 (2500674, 1:1000, Millipore), Anti-H3K27me2 (ab24684, 1:1000, Abcam), Anti-H3K27me3 (07-449, 1:1000, Millipore), anti-EZH2 (5246, 1:1000, CST), anti-Suz12 (sc-271325, 1:1000, Santa Cruz), anti-EED (2514035, 1:1000, Millipore).
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10

Whole Cell Lysate Preparation and Immunoblotting

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Whole cell lysates were prepared by resuspending cells in Nonidet P-40 buffer (50 mm Tris-HCl, pH 8.0, 500 mm NaCl, 1 mm EDTA, 1% Nonidet P-40, 10% glycerol) and sonicated (Bioruptor). Protein concentration was determined using the Bio-Rad DC protein assay (Bio-Rad) and analyzed by a Tecan infinite F200 plate reader (Tecan). Protein samples were subjected to SDS-PAGE. Antibodies used in the study were anti-Ezh2 (Cell Signaling Technology), anti-Tuj1 (Covance), anti-Erk1/2 (Sigma), anti-Suz12 (Abcam), and anti-Eed (Millipore).
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