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36 protocols using anti histone h3

1

Western Blot Analysis of Testicular Proteins

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Western blot was performed using testicular tissue as described in our previous study [33 (link)]. The primary antibodies included anti-activating transcription factor 4 (ATF4, Cell Signaling Technology, Danvers, MA, USA, 1 : 1000), anti-Bcl-2-associated X protein (Bax, Cell Signaling Technology, 1 : 1000), anti-B-cell lymphoma 2 (Bcl-2, Santa Cruz Biotechnology, 1 : 2000), anti-binding immunoglobulin protein (BIP, Cell Signaling Technology, 1 : 1000), anti-caspase12 (Cell Signaling Technology, 1 : 1000), anti-cleaved caspase3 (c-caspase3, Cell Signaling Technology, 1 : 1000), anti-C/EBP homologous protein (CHOP, Cell Signaling Technology, 1 : 1000), anti-GAPDH (Santa Cruz Biotechnology, 1 : 2000), anti-histone H3 (Santa Cruz Biotechnology; 1 : 1000), anti-intercellular adhesion molecule 1 (ICAM-1, Santa Cruz Biotechnology, 1 : 500), anti-inducible nitric oxide synthase (iNOS, Cell signaling Technology, 1 : 1000), anti-NRF2 (Santa Cruz Biotechnology, 1 : 1000), anti-pro-caspase3 (Cell Signaling Technology, 1 : 1000), and anti-vascular cell adhesion molecule 1 (VCAM-1, Santa Cruz Biotechnology, 1 : 500).
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2

Soluble Protein Extraction and Analysis

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For preparation of soluble protein in cell lysates, cells were first washed twice with ice-cold PBS and sonicated in 20 mM Tris, pH 8.0, 150 mM NaCl, 1 mM EDTA, 0.5% (w/v), Nonidet P-40 with protease(s) and 25 mM NaF, 2 mM Na3VO4, 0.1 mM PMSF, and 20 μg/mL aprotinin. The soluble and insoluble fractions were prepared by centrifugation at 15,000 × g for 15 min at 4°C. The soluble proteins were separated by electrophoresis through SDS-polyacrylamide gels (6, 8, and 15% w/v acrylamide) and then electrophoretically transferred to a PVDF membrane. [Subsequently, each membrane was blocked with 5% (w/v) skim milk in Tris-buffered saline containing 0.1% (w/v), Tween-20 for 1 h at room temperature and then hybridized with the appropriate primary antibody (diluted in tris-buffered saline) with gentle agitation overnight at 4°C. After washing three times with this buffer, each membrane was incubated with an appropriate secondary antibody for 1 h at room temperature. Each immunopositive band was visualized with enhanced chemiluminescence detection (GE Healthcare). The following antibodies and chemicals were used: anti-EZH2 (1:1000; BD), anti-H3K27me3 (1:1000; Abcam), anti-histone H3 (1:1000; Santa Cruz Biotechnology), and anti-α-tubulin (1:5000; Sigma); MG-132 was from Millipore, and 3-deazaneplanocin A-HCl was from Cayman Chemical Company. Images were quantified with Image J software.
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3

Western Blotting of Protein Expression

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Fresh tissues and cells were lysed with cell lysis buffer (Beyotime Biotechnology) and western blot was performed as described previously [18 (link)]. Briefly, 40 μg total proteins were applied to separation with SDS–PAGE gel. After the electrophoresis, the proteins were transferred to PVDF membranes (Millipore), followed by blocking in the TBST buffer containing 5% fat-free milk. The membranes were then incubated with indicated antibodies overnight at 4 °C, and then washed and incubated with HRP-conjugated secondary antibodies (Zhongsanjinqiao) for 2 h at room temperature and finally visualized using Chemiluminescent ECL reagent (Vigorous Biotechnology). The following antibodies were used in this work: Anti-GAPDH (Cell Signaling Technology), anti-JMJD2A (Cell Signaling Technology), anti-Histone H3 (Santa Cruz Biotechnology), anti-H3K9me3 (Abcam), anti-H3K36me3 (Abcam), anti-mTOR (Cell Signaling Technology), anti-p-mTOR (Cell Signaling Technology), anti-Akt (Cell Signaling Technology), anti-p-Akt Thr308 (Cell Signaling Technology), anti-S6K1 (Cell Signaling Technology), anti-p-S6K1 (Cell Signaling Technology).
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4

Protein Extraction and Western Blot Analysis

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The proteins in the cells were extracted with Pro-Prep (Intron Biotechnology, Seongnam, Korea) and centrifuged after sonication. A total of 20 μg of each protein was separated with SDS-polyacrylamide gel electrophoresis (PAGE). After the size-dependent separation, the proteins were transferred to polyvinylidene difluoride (PVDF) membranes using semi-dry transfer (Bio-Rad, Hercules, CA, USA). The membranes were incubated with primary antibodies overnight at 4 °C, followed by incubation with horseradish peroxidase (HRP)-conjugated secondary antibodies (Abcam, Cambridge, UK) for 1 h at room temperature. The signals were detected with chemiluminescence reagents (Abclon). Anti-acetyl histone H3 (Merck Millipore, 06-599, Burlington, MA, USA), anti-histone H3 (Santa Cruz Biotechnology, SC-10809, Dallas, TX, USA), anti-acetylated α tubulin (Santa Cruz Biotechnology, SC-23950), anti-tubulin (Santa Cruz Biotechnology, SC-32293), anti-Runx2 (Abcam, ab23981), and anti-Adiponectin (Cell Signaling Technology, #2789, Danvers, MA, USA) were used for the immunoblotting assay in this study. The levels of acetyl H3 and acetylated α tubulin were quantified with ImageJ and normalized to the quantified levels of H3 and α tubulin.
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5

Glucocorticoid Receptor Phosphorylation Analysis

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Cells were washed with PBS and lysed in Trion X-100 lysis buffer (50 mM Tris-HCl pH7.5, 150 mM NaCl, 1% Trion X-100) supplemented with protease inhibitor cocktail (Roche) and phosphatase inhibitor cocktail (Roche). Cell lysates were separated on NuPAGE 4–12% Bis-Tris gels (Invitrogen) and transferred to PVDF membranes (Bio-Rad). Immunoblot signals were developed using SuperSignal West Pico Chemiluminescent Substrates (Pierce Biotechnology). Primary antibodies used in the study included anti-GR antibody (Santa Cruz), anti-GR(Phospho-Ser203) antibody (Assaybiotech), anti-GR(Phospho-Ser211) antibody (Cell signaling), anti-GR(Phospho-Ser226) antibody (Assaybiotech), anti-IKK2 antibody (Cell signaling), anti-histone H3 (Santa Cruz), anti-GAPDH (GeneTex), and anti β-actin antibody (Santa Cruz).
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6

Comprehensive Kidney Protein Analysis

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Western blot was performed using kidney cortex as described in our previous study [25 (link)]. The primary antibodies were anti-KEAP1 (Santa Cruz Biotechnology, Dallas, TX, USA; 1:1,000), anti-NRF2 (Santa Cruz Biotechnology; 1:1,000), anti-Histone H3 (Santa Cruz Biotechnology; 1:500), anti-4-HNE (Alpha Diagnostic, San Antonio, TX, USA; 1:3, 000), anti-3-NT (Millipore, Temecula, CA, USA; 1:1,000), anti-TGF-β1 (Cell Signaling, Beverly, MA, USA; 1:500), anti-COL4 (Abcam, Cambridge, MA, USA, 1:500), anti-FN (Santa Cruz Biotechnology; 1:500), anti-Smad7 (Santa Cruz Biotechnology; 1:1,000), anti-Smad3 (Santa Cruz Biotechnology; 1:1,000), anti-p-Smad3 (Cell Signaling; 1:500), anti-p-JNK (Cell Signaling; 1:500), anti-PDCD4 (Santa Cruz Biotechnology; 1:1,000), anti-t-JNK (Cell Signaling; 1:1,000), anti-Actin (Santa Cruz Biotechnology; 1:2,000) and anti-GAPDH (Santa Cruz Biotechnology; 1:3,000). These antibodies were routinely validated when they arrived from suppliers with previous positive tissues that had been defined either based on the knockout or overexpression of the target protein.
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7

STAT6-Mediated Regulation of ZEB1 Transcription

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HT29 cells were serum-starved overnight and treated with 100 ng/mL IL-13 for 3 h. Cells was cross-linked with 1% formaldehyde, lysed and sonicated. Sheared chromatin was subjected to immunoprecipitation overnight at 4°C with anti-STAT6 or anti-histone H3, or with normal IgG (Santa Cruz). IgG was used as the negative control antibody, whereas anti-histone H3 and the chromatin extract without any antibody treatment were used as the positive controls. Chromatin-antibody complexes were isolated using Protein A/G PLUS-Agarose (Santa Cruz). The crosslinking was reversed and genomic DNA fragments were purified and analyzed by PCR or real-time PCR (qPCR) using the following primer pair for ZEB1 promoter: 5′- CCGGTCACGTTTCAGTTT-3′ (forward) and 5′-TCCTGCTTCCCACCTCCT-3′ (reverse). All of the experiments were repeated at least three times.
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8

ChIP Assay for FGFBP1 Promoter Binding

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ChIP was performed as previously reported25 (link). Briefly, protein–DNA crosslinking was initiated by directly adding formaldehyde to the culture medium at a final concentration of 1%, and cells were incubated for 15 min. Chromatin was prepared using a ChIP Assay Kit (Upstate Biotechnology) according to the manufacturer’s protocol. Equal amounts of chromatin from each sample were incubated overnight at 4 °C with 1 ml of anti-FLAG M2 (Sigma-Aldrich), anti-mouse IgG (Sigma-Aldrich), or anti-histone H3 (Santa Cruz Biotechnology) antibodies.
ChIP recovered DNA was then amplified by qPCR using primers covered a segment containing target region of the FGFBP1 promoter. Primers as follows: FGFBP1-1 (−1.7 kb) forward, 5′-GCAGACGGCAGTCACTAGG-3′; FGFBP1-1 reverse, 5′-CACTCTCGAAGACGCTGCT-3′; FGFBP1-2 (−0.8 kb) forward, 5′-GAACATTTGGGAAATCTCTTGC-3′; and FGFBP1-2 reverse, 5′-TGTGGCTCTGAAGGCAGTT-3′.
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9

ChIP Assay for Sox9 and Col2a1 Regulation

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The chromatin immunoprecipitation assay was performed as previously described (12 (link)). The primers used for the mouse Bbf2h7 promoter were: 5′-GAGGGATCAGGAGTTCAAGCTCAG-3′ (forward) and 5′-GACATTAGCCAATCTTGCCACAC-3′ (reverse), yielding a 176-bp product. The primers used for the mouse Col2α1 enhancer were: 5′-CAGCGATGGCTTCCAGATGGGCTG-3′ (forward) and 5′-GAGGTGGCGGCAGGCGGGCAC-3′ (reverse), yielding a 222-bp product. The following antibodies were used: anti-Sox9 (Santa Cruz Biotechnology), anti-histone H3 (Santa Cruz Biotechnology), and rabbit IgG (Sigma).
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10

Western Blot Analysis of Protein Expression

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WB was conducted according to conventional protocols. Briefly, cells treated as indicated were harvested and lysed using RIPA buffer (Beyotime, China). Proteins were extracted and transferred to nitrocellulose membranes via SDS–PAGE. Then, membranes were blocked with 5% skimmed milk for 1 h at room temperature prior to incubation with primary antibodies overnight at 4 °C. The primary antibodies used were anti-O-GlcNAc (Abcam, #ab2735), anti-OGT (Abcam, #ab184198 or #ab177941), anti-YAP (Abcam, #ab52771), anti-β-Tubulin (CST, #2128), anti-Histone-H3 (Santa Cruz, #sc-10809), anti-TFRC (Abcam, #ab84036), anti-SLC7A11 (Abcam, #175186), and anti-GAPDH (CST, #5176). For nuclear and cytosolic separation, nuclear extraction was conducted according to the manufacturer’s protocols for the Nuclear Extraction Kit (Active Motif, USA). Membranes were incubated with HRP-linked secondary antibodies [anti-rabbit (CST, #7074) or anti-mouse (CST, #7076)] for 1 h at room temperature. Signals were detected using Pierce™ ECL Western Blotting Substrate (Thermo Scientific, USA).
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