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67 protocols using hdac2

1

Isolation and Identification of FC from Ferula assafoetida

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FC (Figure 1A) was isolated and identified from Ferula assafoetida as previously described [12 (link)]. 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), Bcl-2, and β-actin were purchased from Sigma-Aldrich (Sigma-Aldrich, St. Louis, MO, USA). Also, specific antibodies for Cyclin D1, Cyclin E, Cyclin B1 were bought from Santa Cruz Biotechnology (Santa Cruz Biotechnology, Dallas, TX, USA). PARP, HDAC1, and HDAC2 were purchased from Cell Signaling (Cell signaling Technology, Danvers, MA, USA) for Western blot analysis.
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2

Hippocampal Protein Quantification

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To measure the protein concentrations in the hippocampus, we homogenized the tissue in RIPA lysis buffer supplemented with a cocktail of protease and phosphatase inhibitors (Applygen, China) on ice. After centrifugation, the supernatant protein concentration was determined with a bicinchoninic acid (BCA) protein assay reagent kit (Thermo Pierce, USA). After determination of the protein concentration, protein samples were separated by SDS-PAGE and subsequently transferred to PVDF membranes (Bio-Rad, USA). Membranes were blocked with 5% nonfat milk in TBST (0.1% Tween-20 in TBS) and then incubated at 4 °C overnight with primary antibodies: HDAC2 (1:2000, Cell Signaling Technologies, USA), HDAC3 (1:2000, Santa Cruz, USA), HDAC4 (1:2000, Cell Signaling Technologies, USA), HDAC6 (1:4000, Merck Millipore, USA), Acetyl-H3 (1:2000, Merck Millipore, USA), Acetyl-H3K9 (1:2000, Merck Millipore, USA), Acetyl-H3K14 (1:2000, Merck Millipore, USA), BDNF (1:1000, Abcam, UK), c-Fos (1:2000, Merck Millipore, USA), and β-actin (1:2000, Santa Cruz, USA). After being rinsed with TBST, the membranes were incubated with horseradish peroxidase-conjugated secondary antibodies (1:1000, Beyotime Institute of Biotechnology, China). Protein bands were visualized with an ECL detection system (Beyotime Institute of Biotechnology, China) and quantified with ImageJ software (NIH).
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3

Western Blot Analysis of Protein Complexes

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Western blot was performed according to the manufacturer’s protocol. Equal amounts of protein were subjected to sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS–PAGE) gels followed by transfer to PVDF membranes. Membranes were probed with primary antibodies overnight and then washed and incubated with horseradish peroxidase (HRP)-conjugated-secondary antibodies. Detection was performed by the enhanced chemical luminescence (ECL) method. The primary antibodies of NCOR2 (ab24551; 1:1000) was purchased from Abcam. CRBN (NBP1-91810; 1:1,000) antibody was purchased from Novus Biologicals. c-Myc (#5605; 1:1,000), IKAROS (#9034; 1:1,000), MTA1 (#5647; 1:1,000), MBD3 (#14540; 1:1,000), HDAC1 (#5356; 1:1,000), and HDAC2 (#5113; 1:1,000), antibodies were purchased from Cell Signaling Technology, Inc.
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4

Immunoblotting of HDAC Isoforms

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Immunoblotting was performed as previously described(16 (link)). Briefly, pediatric human and neonatal rat RV homogenates were prepared and concentrations quantified as above for HDAC catalytic activity assay. Proteins were resolved by SDS-PAGE, transferred to nitrocellulose membranes (BioRad) and probed with antibodies for HDAC1 (Cell Signaling Technology, 5356), HDAC2 (Cell Signaling Technology, 5113), HDAC3 (Cell Signaling Technology, 3949), HDAC4 (Cell Signaling Technology, 5392), HDAC5 (Cell Signaling Technology, 2082), HDAC6 (Santa Cruz Biotechnology, 11420), HDAC7 (Cell Signaling Technology, 2882), calnexin (Santa Cruz Biotechnology, 11397).
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5

Western Blot Analysis of Muscle Proteins

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C2C12 cells and gastrocnemius muscle were lysed with RIPA buffer (Solarbio, Beijing, China); the protein concentrations were measured by a BCA kit (Beyotime, Shanghai, China). Then, 40 µg of the samples were electrophoresed in 10–12% SDS polyacrylamide gels and electrically transferred to 0.2-µm PVDF membranes (Millipore, USA). The membranes were immersed and incubated in 5% fat-free milk at room temperature for 1 hour. The membranes were then incubated with primary antibodies against HDAC2, P53, P21, IKK, and NF-κBp65 (1:1000, Cell Signaling Technology, USA) and MURF1, MAFbx, and SMP30 (1:1000, Abcam, UK) overnight at 4°C, followed by incubation with fluorescent secondary antibodies (1:1000, Cell Signaling Technology, USA). The GAPDH antibody (1:1000, Cell Signaling Technology, USA) was used as the control. Fluorescence signal detection was performed with an infrared imaging instrument (Odyssey, USA), and protein expression was quantified by densitometry analysis with ImageJ software.
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6

Histone Modification Profiling in A2780 Cells

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The A2780 cell line was purchased from American Type Culture Collection (ATCC), and SAHA was purchased from Selleckchem (Houston, TX, USA). Primary antibodies against Ac-H2A, Ac-H2B, Ac-H3, Ac-H4, HDAC2, HDAC3, HDAC4, DNMT3A, PRMT1, SUV39H1, MDMX, p53, p21WAF1/CIP1, p27Kip1, AURKB, CDC25C, GADD45A (1:1000) and Alexa Fluor 488 dye were purchased from Cell Signaling Technology (Danvers, MA, USA). The MDM2 antibody (1:500) was purchased from Santa Cruz Biotechnology (Dallas, TX, USA). β-actin (1:5000), secondary antibodies (anti-rabbit, anti-mouse), horseradish peroxidase (HRP) conjugate, and dimethyl sulfoxide (DMSO) were purchased from Sigma Aldrich (St. Louis, MO, USA). Nitrocellulose membrane (NC) (0.45 µm) was purchased from Amersham (GE Healthcare Life Sciences, Marlborough, MA, USA) and KPL LumiGlo Reserve chemiluminescent substrate was purchased from SeraCare Life Sciences (Milford, MA, USA).
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7

Assessing HDAC-Sin3a Interaction in Heart

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Protein extracts were prepared in RIPA lysis buffer (Thermo Fisher Scientifics) from snap-frozen heart tissues or NRCMs. Protein concentration was measured by BCA assay (Thermo Fisher Scientifics). The protein electrophoresis were performed on 4–12% Bis-Tris NuPage gels (Thermo Fisher Scientifics). The Bio-Rad Trans-Blot Turbo Transfer System was used for the proteins transfer to nitrocellulose membranes. Secondary antibodies used were from LI-COR Biosciences. The blots were quantified using Image J or LI-COR Image studio Lite. HDAC1, HDAC2 and HDAC3 antibodies were from Cell Signaling Technologies (Cat#5356, #5113 and #3949 respectively). The Sin3a antibody was from Abcam, # ab129087.
Co-immunoprecipitation: HDAC1 was immunoprecipitated from 500μg heart lysates (in RIPA buffer) using 0.5μg HDAC1 antibody (Cell Signaling Technologies Cat#5356), and 25 μl Dynabeads™ Protein G (Thermo Fisher Scientifics). Co-immunoprecipitated HDAC2 and Sin3a were probed using antibody from Cell Signaling Technologies (#5113) and Abcam (# ab129087) respectively.
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8

Immunoblot Analysis of Apoptosis Regulators

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Immunoblots were carried out as described by our group [23 ,24 (link)]. Original immunoblots see File S1. Antibodies used for this assay were: BCL-XL (#ab32370), survivin (#ab134170), p21 (#ab109520), BAX (#ab32503), BAK (#ab32371), BIM (#ab32158), HDAC3 (#ab32369), GAPDH (#ab128915) from Abcam, Cambridge, UK; MCL-1 (#sc-819), HDAC8 (#sc-374180), HSP90 (#sc-13119), vinculin (#sc-73614) from Santa Cruz Biotechnology, Heidelberg, Germany; cleaved caspase-3 (#cs9661), PARP1 (#cs9542), BID (#cs2002), HDAC1 (#cs34589), HDAC2 (#cs5113), histone H3 (#cs14269), ac-histone H3 (K9) (#cs9649), ac-histone H3 (K18) (#cs9675), ac-histone H3 (K27) (#cs8173) from Cell Signaling, Leiden, The Netherlands; ac-tubulin (#T7451) from Sigma-Aldrich, Taufkirchen, Germany; ac-histone H3 (#06-599) from Merck Millipore, Burlington, MA, USA; and NOXA (#ALX-804-408) from Enzo Life Sciences, New York, NY, USA. HSP90, GAPDH, and vinculin served as independent housekeeping proteins to normalize protein loading. The protein ladders used were the PageRulerTM pre-stained protein ladder (#26616) and the PageRulerTM Plus pre-stained protein ladder (#26619) from Thermo Fischer Scientific, Waltham, MA, USA.
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9

Western Blot Protein Detection Protocol

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Western blot was performed as described (24 (link)). Cell extracts or eluted proteins were separated by 4–12% Bis-Tris polyacrylamide gel electrophoresis (PAGE) (Invitrogen). Proteins were transferred to polyvinyliden difluoride (PVDF) membrane (GE Amersham, Hybond-C or Millipore, Immobilon-FL) and blocked for 1 h at room temperature with 5% non-fat dry milk in TBS-T buffer (20 mM Tris, 150 mM NaCl, 0.1% Tween20, pH 7.4). The membranes were then incubated with primary antibodies to HDAC1 (Cat# 5356s, Cell Signaling Technology), HDAC2 (Cat# 5113s, Cell signaling Technology), PRDM1 (Cat# 9115s), hnRNPM (Cat# SAB1404107, Sigma Aldrich), TP53BP1 (Cat# 4937s, Cell Signaling Technology), β-Actin (Cat# ab8226, Abcam), V5 (Cat# MA5-15253, Sigma Aldrich), and Flag (Cat# F1804, Sigma Aldrich) overnight at 4°C. Proteins bound by antibody were visualized by ECL (Thermo Scientific, # 34580 or Advansta, K-12045) and sapphire biomolecular imager (Azure Biosystems).
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10

Comprehensive Protein Expression Profiling

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Whole-cell lysates, harvested with RIPA buffer containing protease and phosphatase inhibitors, were run on 4–15 % SDS-PAGE gradient gels (Biorad). Blots were blocked in 5 % milk, then probed with antibodies; CD326 (Cell Signaling#2929 S), CD166 (Abcam#ab49496), CD44(2c5) (R&D#BBA10), BMI-1 (Cell Signaling#2830 S), HDAC1 (Cell Signaling#5356), HDAC2 (Cell Signaling#5113), HDAC3 (Cell Signaling#3949), HDAC4 (Cell Signaling#7628), HDAC5 (Cell Signaling#2082), HDAC6 (Novus#91805), HDAC7 (Abcam#ab12174), HDAC8 (Novus#91807), HDAC9 (Abcam#ab18970), HDAC10 (Novus#91801). Blots were developed using SuperSignal West Pico or Femto ECL (ThermoScientific). All experiments were repeated a minimum of three times.
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