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19 protocols using anti histone 3

1

Immunoblotting of Endogenous COP1 Protein

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To detect endogenous COP1 protein levels, an anti-COP1 polyclonal antibody was used (Lee et al., 2017 (link)). Fresh seeds (harvested within 1 month before use) were imbibed in distilled water with or without 10 μM GA3 or 10 μM PAC, and harvested at each time point. Total crude extracts were prepared using extraction buffer containing 50 mM Tris–HCl pH 7.5, 4 M urea, 150 mM NaCl, 1 mM EDTA, and protease and phosphatase inhibitor mixtures (1 mM PMSF, 5 μg/mL leupeptin, 5 μg/mL aprotinin, 5 μg/mL pepstatin, 5 μg/mL antipain, 5 μg/mL chymostatin, 2 mM Na2VO3, 2 mM NaF, and 50 μM MG132), separated by SDS-PAGE, and then immunoblotted with anti-COP1, and anti-Histone 3 (Abcam) antibodies.
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2

Quantifying Protein Levels in Synchronized Parasites

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At the late trophozoite stage synchronized parasites were treated with 0.5μM Shld1 or ethanol solvent control for 36h. Proteins were sequentially extracted as previously described2 (link), separated on 4-12% polyacrylamide gels (Life Technologies), and assayed using anti-HA tag (Roche Diagnostics 11 867 423 001), anti-Histone 3 (Abcam ab1791), and anti-PfPP2c (generous gift from C. Ben Mamoun). Replicates were biological not technical.
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3

Signaling Pathway Protein Analysis

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Cells were washed with ice-cold phosphate-buffered saline (PBS) and then solubilized with protease inhibitor (Upstate Biotechnology, Temesula, CA, USA)-containing RIPA buffer. Lysates were immunoblotted with indicated antibodies, anti-G9a, anti-DUSP4, anti-p-AMPK, anti-AMPK, anti-S6K and anti-p-S6K (T389) (Cell Signaling Technology), anti-H3K9me1 (Millipore, MA, USA), anti-GLP, anti-H3K9me2, anti-histone 3, anti-LC3B (Abcam), anti-H3K9me3, anti-caspase 3, anti-PARP, anti-p62, anti-β-actin anti-GAPDH, anti-α-tubulin (GeneTex), anti-p-Akt, anti-Akt, anti-p-ERK and anti-ERK (Santa Cruz Biotechnology, Santa Cruz, CA).
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4

Protein Quantification and Verification

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1-2 million cells (up to 5 million cells for PCID2 knockdown western blot) were lysed using an NP-40 IP lysis buffer (1% NP-40, 25mM Tris pH 7.4, 150 mM NaCl, 1mM EDTA, 5% glycerol, 1 U/mL EDTA-free protease inhibitor cocktail (Roche) and 1mM DTT) for 30 minutes on ice and centrifuged for 10 minutes at 14000 rpm in a cold centrifuge. Supernatants were collected, 1x Laemmli loading buffer was added and lysates were boiled for 5 min at 95°C and subjected to 12% SDS-PAGE separation. The following antibodies were used for detection of proteins by western blot: anti-M2-FLAG (Sigma, F3165), anti-β-tubulin (Sigma, T5168), anti-PCID2 (Genetex, GTX52023) and anti-Histone 3 (Abcam, ab1791) antibodies.
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5

Immunostaining of Drosophila Embryos

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Embryos were collected on grape agar plates, dechorionated for 2 min in 50% bleach, and fixed in methanol-heptane (1:1) for 5 min. The fixed embryos were stored in methanol at −20°C. Before immunostaining, the embryos were first rehydrated gradually (5 min each in 1:3, 1:1, and 3:1 PTA:methanol and then 10 min in PTA). PTA consisted of PBS supplemented with 0.1% Triton X-100, and 0.02% azide. The embryos were then blocked in PBTA (PTA plus 1% BSA) for 30 min and incubated with primary antibodies (1:100 in PBTA) for 1 h at room temperature or overnight at 4°C. The following primary antibodies were used: anti-Histone 3 (Abcam, ab1791), anti-H3K9me1 (Active Motif, 39249), anti-H3K9me2 (Active Motif, 39683 and 39375), anti-H3K9me3 (Active Motif, 39765; Millipore, clone CMA308), anti-H3K9ac (Abcam, ab10812), anti-H3K27ac (Abcam, ab4729), anti-H3K27me3 (Cell Signaling, 9733), and anti-H4ac (Millipore, 06-598). The embryos were washed three times for 5 min each in PBTA and incubated with the appropriate fluorescently labeled secondary antibodies (Molecular Probes) for 1 h in the dark at room temperature. They were then washed four times for 5 min each in PBTA and mounted in VectaShield mounting medium with DAPI (Vector Laboratories). For TALE-light stainings, GFP- or mCherry-tagged purified TALE-light protein (1:500) was included during the incubation with secondary antibodies.
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6

Characterizing DNA Damage Response

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For siRNA knockdowns, 293T or U2OS cells were seeded in a six-well plate format and transfected with 20 nM FTO siRNAs (ON-TARGET plus FTO SMARTpool, Dharmacon) or non-target control siRNAs (ON-TARGET plus non-targeting pool, Dharmacon) with Lipofectamine RNAiMAX (ThermoFisher) following manufacture's protocol. 48 h after transfection (or 24 h after seeding for WT and FTO KO cells), 2 mM hydroxyurea (HU) or 1 μM camptothecin (CPT) were added to the cell culture medium and cells were collected after the indicated hours. Western blotting was performed with the following antibodies: Anti-FTO (Abcam, ab126605), Anti-γ-H2AX (Sigma, 05-636-I), Anti-tubulin (Sigma, T6074), Anti-histone 3 (Abcam, ab1791), Anti-pSer317 Chk1 (Merk, DR1025), Anti-pRPA(S4/S8) (Bethyl, A300-245A). Quantification of western blot signals were performed using the software ImageJ.
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7

Antibodies for Cell Cycle Analysis

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Rabbit polyclonal affinity–purified anti-Cyclin Ba/b (acetyl-NRDLNIQESGPVKAVVNAC-amide; acetyl-CLEFLRRFSRVAEETIDPKEY-amide), anti-CDK1b (acety1-CPDFTKPSTLNVNTSLNEMDM-amide), anti-CDK1c (acetyl-MRKRNIDRPPTQDLNNYC–amide), ant-CDK1d (acety1-MIKAKSGTQDLSNYKRC-amide), and anti-lamin1 (acetyl-QSPISLPPLSGSTC-amide) were from 21st Century Biochemicals (Marlboro, MA). Other antibodies: anti-PSTAIR (Abcam, ab10345), anti-ATPB (Abcam, ab37922), anti-histone 3 (Abcam, ab10799), anti-H3-S28 (Abcam, ab10543), anti-GFP (AMS biotechnology, M30939-2). Secondary antibodies for immunofluorescence: goat anti-rabbit IgG (H+L) Alexa Fluor 568 (Thermofisher, A-11011); and for western blots: goat anti-rabbit IgG (H+L) superclonal™ secondary antibody, HRP (Thermofisher, A27033), Peroxidase-AffiniPure Goat Anti-Mouse IgG (H+L) (Jackson ImmunoResearch, 115-035-003).
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8

Synthesis and Characterization of Telmisartan-Labeled Probes

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2-Cl-trityl chloride resin (loading: 0.939 mmol/g), fmoc-amino acids and o-benzotriazol-1-yl-N, N, N', N'-tetramethyluronium hexafluorophosphate (HBTU) were bought from GL Biochem (Shanghai). 4-Chloro-7-nitrobenzol-2-oxa-1, 3-diazole (NBD-Cl) and telmisartan were purchased from Sigma-Aldrich (USA). Cy5.5 NHS ester was obtained from APExBIO (USA). Recombinant MAS1 Protein (2 µg) was obtained from Abnova (China). Fetal bovine serum (FBS), Dulbecco's modified Eagle's medium (DMEM), trypsin, and Penicillin-streptomycin were obtained from Thermo Fisher (USA). DHE fluorescence probe, Apoptosis Analysis Kit, DAPI, and Hoechst 33342 dye were purchased from Molecular Probes (USA). CCK-8 kit was purchased from Dojindo Co. Ltd (Japan). The primary antibodies of anti-AT1R, anti-α-SMA, anti-Bax, anti-Bcl-2, anti-Histone 3, anti-Collagen I, anti-TGF-β1 and anti-cTnT were obtained from Abcam (Britain). The antibodies of anti-AKT, anti-p-AKT, anti-P65, anti-Caspase3 were purchased from Cell Signaling Technology (USA). ELISA kit for IL-6, TNF-α, CRE, ALT, TGF-β1 were bought from MSKBIO (China). All other solvents and reagents were commercially available and used without further purification, unless noted otherwise.
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9

Protein Extraction and Histone Modification Analysis

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Similar procedures were conducted in our previous work (Lan et al., 2016 (link)). The strains were incubated at 28 °C for 72 h, and the mycelia of each sample were collected, then frozen in liquid nitrogen and ground into powder. Next, 100 mg powder was dissolved in 1 mL radio immuno precipitation assay lysis buffer (RIPA, Beyotime, Shanghai, China), which was used to extract the whole proteins. The concentrations of the protein extracts were measured using a Nanodrop detector and then diluted. We uploaded 40 μg of total protein and separated them by 15% sodium dodecyl sulfate polyacrylamide gel electrophoresis. The proteins were then transferred to a polyvinylidene fluoride membrane (Millipore, USA). We used the specific antibodies anti-actin (1:5000 dilution, Cell Signaling Technology), anti-Histone3 (1:5000 dilution, Abcam), anti-acetyl-histone3 (H3ac, 1:5000 dilution, Abcam), anti-acetyl-H3K56 (H3K56ac, 1:5000 dilution, Active Motif), and anti-acetyl-H3K9 (H3K56ac, 1:5000 dilution, PTM Biolabs) to detect histone modifications.
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10

Quantitative Analysis of Protein Expression

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The total protein from liver tissues and hepatocytes was extracted and homogenized in RIPA buffer (Beijing Solarbio Science & Technology Co., Ltd.). The concentrations of the extracted nuclear and cytoplasmic fractions were quantified using the bicinchoninic acid assay method. A total of 50 µg protein per sample was separated by SDS-PAGE (10%) and then transferred to a PVDF membrane, prior to blocking with 5% non-fat milk in 1X TBST, overnight at 4°C. The membrane was then incubated with anti-β-catenin (1:1,000; product no. ab32572), anti-β-actin (1:5,000; product no. ab8227), anti-histone 3 (1:2,000; product no. ab62642; all from Abcam) primary antibodies for 2 h at room temperature. After washing three times in 1X TBST, the membranes were incubated with the corresponding HRP-conjugated secondary antibody (1:5,000; cat. no. A6154-1 ml; Sigma-Aldrich; Merck KGaA) for 1 h at room temperature. The membranes were washed once more, exposed to ECL (Sangon Biotech Co., Ltd.), and then photographed by ChemiDoc™ XRS+ Imaging system (Bio-Rad Laboratories, Inc.). The protein expression levels were quantified using ImageJ software version 1.46 (National Institutes of Health). Histone 3 and β-actin were used as internal controls.
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