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7 protocols using acetyl histone h4

1

Resveratrol Modulates Smad Signaling

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Confluent fibroblasts were preincubated in serum-free DMEM with 100 µM resveratrol for 24 hours prior to addition of TGFβ (10 ng/ml) for 60 minutes. Whole-cell lysates were prepared and immunoprecipitated with anti-Smad1/2/3 antibodies (Santa Cruz Biotechnology) and subjected to immunoblot analysis.
ChIP assays were performed using antibodies against p300 (Santa Cruz Biotechnology) and acetyl histone H4 (Cell Signaling Technology) with EZ Magna ChIP Assay Kits (Upstate/Millipore) (19 (link)). Real-time qPCR amplification of the captured DNA sequences was performed using primers complementary to human COL1A2 DNA sequences flanking the Smad-binding element (19 (link)). The results were normalized to input DNA.
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2

Western blot analysis of cellular signaling

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Western blot assay was performed using whole cell lysates from either liver tissue or hepatocytes, or media as previously described (4 (link)). Membranes were incubated overnight using the following antibodies: HMGB1 (Abcam) and β-actin (Sigma); phospho-p38, p38, phospho-JNK, JNK, ERK, phospho-ERK, p65, phospho-p65, PARP-1, acetyl-histone H3, acetyl-histone H4, and phospho-histone H2A.X (Cell Signaling); PAR (BD bioscience).
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3

Synergistic effects of SAHA and ATO on K562 cells

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SAHA was kindly provided by Dr. Defu Zeng (City of Hope National Medical Center, Duarte, California, USA). DMSO was diluted to a concentration of 10 mmol/L. ATO was purchased from Heilongjiang Harbin Medical University Pharmaceutical Co., Ltd., and diluted to a concentration of 2 mmol/L. Both SAHA and ATO were stored at −20 °C. RPMI 1640 was purchased from Gibco (Grand Island, New York, USA); fetal bovine serum was purchased from TBD (TBD Science, China); penicillin/streptomycin was purchased from Hyclone (Logan, Utah, USA); an apoptosis detection kit (Annexin-V-FITC, PI double staining) was purchased from Roche (Basel, Switzerland); Protein Extraction reagents were purchased from Wuhan Boster Biological Co., Ltd. (Wuhan, China); antibodies against c-abl, p21, Acetyl-Histone H3 and Acetyl-Histone H4, and other proteins were purchased from Cell Signaling Technology (Danvers, Massachusetts, USA). The K562 cell line was preserved and cultured in Fujian Institute of Hematology with a standard protocol as previously described (Liu et al., 2012 (link); Lin et al., 2010 (link)).
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4

Multimodal Regulation of Cell Pathways

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Gossypol (GOS), valproic acid sodium salt (VPA), Tween 80, suberoylanilide hydroxamic acid (SAHA), tubacin, 3-methyladenine (3-MA), propidium iodide (PI), dimethyl sulfoxide (DMSO), Hoechst 33342, and MG132 were purchased from Sigma-Aldrich (St. Louis, MO, USA). GOS was dissolved in dimethyl sulfoxide (DMSO). The final concentration of DMSO never exceeded 0.2%, which had no cytotoxicity in this study (data not shown). WST-1 assay kit was obtained from Roche (Penzberg, Germany). RNase A, Dulbecco's modified Eagle's medium (DMEM), RPMI-1640, fetal bovine serum (FBS), penicillin and streptomycin were purchased from Invitrogen (Carlsbad, CA, USA). Polyvinylidene difluoride (PVDF) membranes (Hybond-P) were purchased from GE Healthcare Life Sciences (Piscataway, NJ, USA). The antibodies against cyclin A2 (#4656), Bcl-2 (#2870), Bax (#2772), Bim (#2933), PARP(#9532), cleaved caspase-3 (#9664), cleaved caspase-8 (#9496), cleaved caspase-9 (#7237), phospho(p)-Akt (Thr308: #2965), Akt (#2920), FOXO3a (#2497), p-FOXO3a (Ser253: #9466), acetyl-histone H3 (Lys9: #9649), acetyl-histone H4 (Lys16: #8804), histone H3 (#9717), LC3B (#3868), and β-tubulin (#2128) were obtained from Cell Signaling Technology (Danvers, MA, USA). The antibody against survivin (sc-10811) was from Santa Cruz Biotechnology (Santa Cruz, CA, USA).
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5

Plasmid and siRNA Transfection Protocols

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Expression plasmids and pBabe-puro retroviral vectors for FLAG- and GFP-tagged TIF-IA and for GFP-, ER- or FLAG-tagged Suv4-20h2 have been described (20 (link)). Expression plasmids for GFP-CHD4 and Nedd4-GFP were gifts from Alexander Brehm and Hiroshi Kawabe, respectively. PAPAS-targeting siRNAs (SilencerSelect, Life Technologies) cover sequences −78/−98 and −100/−121, CHD4 siRNAs were siGENOME SMART pools from Dharmacon (M-052142-01-0005). About 10–40 nM siRNAs were transfected into NIH3T3 cells using RNAiMAX transfection reagent (Life Technologies). Cells were harvested 36–48 h post-transfection. Antibodies against UBF, nucleolin, ERα, CHD4, MTA2 and HDAC1 were from Santa Cruz, antibodies against FLAG-epitope (M2), β-actin, β-tubulin and BrdU were from Sigma-Aldrich. Histone-specific antibodies (H3, H3K9me3, H3K4me3, H4K20me3) were from Diagenode or from Merck Millipore (acetyl-histone H4), the antibody recognizing the phosphorylated CK2 target motif (pSDXE) was from Cell Signaling Technology (CST).
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6

Investigating Histone Modifications

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Insulin, TO901317, AA, and TSA were purchased from Sigma Aldrich (St. Louis, MO, USA). Anti-ACC, acetyl-histone H3, acetyl-histone H4, histone H2A, and HDAC5 antibodies were purchased from Cell Signaling Technology (Danvers, MA, USA). Anti-SREBP1, α-Tubulin, HDAC1, HDAC2, HDAC7, and HDAC10 antibodies were obtained from Santa Cruz Biotechnology (Santa Cruz, CA, USA).
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7

Comprehensive Protein Analysis Protocol

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TEAD4 (#ab58310), pan-OXPHOS (#ab110413), and Ki67 (#ab15580) were purchased from Abcam. p-mTOR (T2446) (#09-345) and acetyl-histone H3 (#06-599) were purchased from Millipore. Phosphor-PGC1a (#AF6650) was purchased from R&D. mTOR (#2938), p-mTOR (S2448) (#5536), YAP (#14074), p-YAP (S127) (#13008), p-YAP(S397) (#13619), p38 (#8690), p-p38 (T180/182) (#4511), acetyl-histone H3 (Lys9) (#9649), acetyl-histone H3 (Lys14) (#7627), acetyl-histone H3 (Lys18) (#13998), acetyl-histone H3 (Lys27) (#8173), acetyl-histone H3 (Lys56) (#4243), histone H3 (#4499), acetyl-histone H2A (Lys5) (#2579), acetyl-histone H2B (Lys5) (#12799), histone H2A (#12349), histone H2B (#12364), acetyl-histone H4 (Lys5) (#8647), acetyl-histone H4 (Lys8) (#2594), acetyl-histone H4 (Lys12) (#13944), acetyl-histone H4 (#2935), PGC-1a (#2178), p21 (#2974), and p27 (#83630) were purchased form Cell Signaling. All antibodies were used at a dilution of 1:1000 for immunoblotting and 1:250 for immunofluorescent staining.
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