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7 protocols using anti histone 3

1

Histone and Actin Immunoblotting

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Samples were boiled in a sodium dodecyl sulphate (SDS) buffer containing dithiothreitol (DTT) and resolved by polyacrylamide gel electrophoresis (SDS-PAGE) on a Criterion TGX precast gel (Any-KD; Bio-Rad Laboratories). Proteins were then transferred to a PVDF membrane (Bio-Rad Laboratories) via semi-dry transfer. The membrane was blocked with 5% bovine serum albumin (BSA; Fisher Scientific) in Tris-buffered saline with 0.1% Tween 20 (TBS-T). H3 was detected with anti-histone 3 (Milipore) and HRP–conjugated goat anti-rabbit (Thermo Scientific). Actin was detected with anti-actin (Milipore) and HRP–conjugated donkey anti-mouse (Thermo Scientific) antibodies.
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2

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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3

Quantification of Protein Levels and Epigenetic Modifications

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Protein was extracted using cell lysis buffer (Cell Signaling) plus PMSF (600μM) and inhibitor of phosphatases (100x). Protein concentration was quantified using the BCA Protein Assay (Pierce). Protein samples were resolved on SDS polyacrylamide gels (Bio-Rad) and subsequently transferred to nitrocellulose membranes by semi-dry transfer using the Trans-Blot Turbo (Bio-Rad). The following antibodies were utilized: subunit 70 kDa (SDHA) antibody from MitoSciences (abcam), COXII antibody from Invitrogen, anti-AMPK and anti-p-AMPK from Cell Signaling, anti-ATPIF1 from Sigma, HIF-1α (BD Transduction Laboratories, Clone 54/HIF-1), β-actin and α-tubulin (Sigma). To assess changes in epigenetics marks, nuclear extracts were prepared using the nuclear complex Co-IP kit from Active Motif and the following antibodies were used: anti-Histone H3K27ac and anti-Histone H3K14ac from Active Motif, anti-Histone H3K18ac, anti-Histone H3K9ac, anti-Histone H3 (tri methyl K4) and anti-Histone H3 (tri methyl K9) from Abcam, anti-Histone H3 (tri methyl K27) and anti-Histone 3 from Millipore. Anti-rabbit 800CW and anti-mouse 680RD from Licor were used as secondary antibodies. Image Studio Lite version 3.1 (Licor) was used for analysis and quantification of protein levels.
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4

Western Blot Analysis of Histone 3

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Samples (protein extracts or plasma) were boiled in a sodium dodecyl sulphate (SDS) buffer containing dithiothreitol (DTT) and resolved by polyacrylamide gel electrophoresis (SDS-PAGE) on a Criterion TGX precast gel (Any-KD; Bio-Rad Laboratories). Proteins were then transferred to a polyvinylidene difluoride (PVDF) membrane (Bio-Rad Laboratories) via semi-dry transfer. Non-specific binding was blocked with 5% bovine serum albumin (BSA; Fisher Scientific) in tris-buffered saline with 0.1% Tween 20 (TBS-T). The membranes were blotted with anti-histone 3 (Milipore) and detected with HRP–conjugated goat anti-rabbit (Thermo Scientific). Finally, the membranes were incubated with enhanced chemiluminescent substrate (ECL; Thermo Fisher Scientific) and imaged with a chemiluminescence imaging systems (Bio-Rad) or developed after exposure onto an X-ray film (Kodak) and digitally scanned.
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5

Quantifying NF-kB Transcription Factors

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To analyze the level of NF-kB, whole-cell, cytoplasmic, and nuclear proteins were extracted. Nuclear proteins were extracted using the NucBuster Protein Extraction kit (Novagen, Rockland, MA, USA). Briefly, 2!10 7 RAW264.7 cells were lysed with 150 ml of reagent 1 to remove cytoplasmic proteins. The pellet was resuspended in 1 ml of 100! Protease Inhibitor Cocktail, 1 ml of 100 mM DTT, and 75 ml of reagent 2. The nuclear protein extracts were collected using centrifugation at 16 000 g for 5 min at 4 8C.
A total of 40 mg of protein was mixed with 5!SDS-PAGE Sample loading buffer (Beyotime), boiled at 100 8C for 5 min. Proteins were transferred to PVDF membranes by electroblotting. The membranes were blocked using 5% non-fat dry milk in TBST for 1.5 h and then probed with anti-P50 (1:5000, Millipore, Billerica, MA, USA), anti-P65 (1:2000, Millipore), anti-IkBa (1:1000, Cell Signaling Technology, Danvers, MA, USA), anti-PIkBa (1:1000, Cell Signaling Technology), anti-histone 3 (1:5000, Millipore). Primary antibodies were detected using the DyLing TM800 Labeled Antibody to Rabbit/Mouse IgG (HtL) (1:10 000, KPL, Gaithersburg, MD, USA). Bound complexes were measured using the Odyssey Infrared Imaging System.
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6

Protein Extraction and Western Blot Analysis

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Total protein was extracted from cells with RIPA buffer (Beyotime, China). Nuclear protein and cytoplasmic protein were extracted with a nuclear cytoplasmic protein extraction kit (Beyotime, China). All protein concentrations were measured by BCA protein assay kit (Beyotime, China). Approximately 40 μg protein extract per sample was separated using a SDS polyacrylamide gel and transferred onto the PVDF membrane (Millipore, USA), and 5% bovine serum albumin was used to block membrane. The membranes were incubated with rabbit anti-GFP (1:1000, Beyotime, China), anti-β-catenin (1:1000, Cell Signaling, USA), anti-Survivin (1:1000, Abcam, USA), anti-cyclin D (1:1000, Cell Signaling, USA), anti-c-myc (1:1000, Abcam, USA), anti-β-catenin Ser45 phosphorylation (1:1000, Cell Signaling, USA), and mouse antibody against β-actin (1:10,000, Sigma, USA), anti-Histone 3 (1:1000, Sigma, USA) overnight at 4°C, followed by incubation for 1hr with horseradish peroxidase (HRP)-conjugated secondary antibodies (1:10,000). After extensive washing in TBST, the expression levels of the protein were detected by Quantity-one software (Bio-Rad Laboratories, USA) using the ECL kit.
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7

DLBCL Protein Expression Analysis

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Normal germinal center (GC) B-cells, DLBCL cell lines or primary DLBCL specimens were lysed using RIPA lysis buffer containing complete protease inhibitor cocktail to prepare whole cell lysates or for immunoprecipitation (IP). Whole cell lysates or IP products were resolved by SDS-PAGE, transferred to PVDF membrane (Bio-Rad), and probed with the indicated primary antibodies: anti-SIRT3, anti-GRP75, anti-Acetylated histone 3, anti-Acetylated lysine, anti-LC3 andanti-p62 were from purchased from Cell signaling technology; anti-ACTB, anti-histone 3, and anti-GDH antibodies were purchased from Sigma, Abeam and Proteintech Group respectively. Membranes were then incubated with a corresponding peroxidase-conjugated secondary antibody. Protein signals were detected using enhanced chemiluminescence. Densitometry values were obtained by using ImageJ 1.44o.
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