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5 protocols using anti h4k16ac

1

Histone Modification Analysis Protocols

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The antibodies used in this study were as follows: anti-H2AS129p (Millipore; catalog no. 07-745-I), anti-H3 (Abcam; catalog no. ab1791), anti-H4 (Millipore; catalog no. 05-858), anti-H3K4me3 (Active Motif; catalog no. 39159), anti-H3K9ac (Active Motif; catalog no. 39137), anti-H4K16ac (Active Motif; catalog no. 39167), and anti-RNA polymerase II (BioLegend; catalog no. 664903).
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2

Histone Acetylation Profiling

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20 amino acids were purchased from EMP Millipore. Site specific primary antibodies include anti-H3K9ac (Cell Signaling), anti-H3K14ac (EMP Millipore), anti-H3K18ac (EMP Millipore), anti-H3K23ac (EMP Millipore), anti-H3K27ac (Cell Signaling), anti-H4K16ac (Active Motif) antibodies, as well as anti-histone H3 (Abcam). Secondary antibody as HRP-conjugated anti-rabbit antibody from Cell Signaling. H4K16ac nucleosome was purchased from Epicypher. The free enzyme HDAC1 (in the complex with HSP70) is purchased from BPS Bioscience.
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3

Protein Analysis by Western Blot

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Samples were loaded on 4–20% gradient TGX Gels (Biorad). Coomassie staining was performed with Novex™ SimplyBlue™ SafeStain (Invitrogen) following the manufacturer’s protocol. Silver staining was performed with Silver Stain SNAP Kit (Pierce) following the manufacturer’s protocol. The primary antibodies used for western blot analyses were anti-Flag HRP-conjugated (Sigma A8592), anti-GFP HRP-conjugated (Fisher Scientific MA5–15256-HRP), anti-H3K9me2 (Abcam 1220), anti-H3K9me3 (Active Motif 61013), anti-H3 (Abcam 1791), anti-H3K4me3 (Abcam 8580), anti-H3K36me3 (Abcam 9050), and anti-H4K16ac (Active Motif 39167).
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4

ChIP Assay for HDAC7 and Histone Modifications

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For ChIP assays, purified CD19+ B or pro–B cells from the bone marrow of Hdac7+/− and Hdac7fl/− mice were cross-linked with 1% formaldehyde and subjected to immunoprecipitation after sonication. ChIP experiments were performed using the LowCell# ChIP kit (Diagenode) according to the manufacturer’s instructions. The following antibodies were used: anti-HDAC7 (Abcam), anti-MEF2C (Cell Signaling Technology), anti-H3Ac(K9/K14) (EMD Millipore), anti-H4K16Ac (Active Motif), anti-H3K27me3 (EMD Millipore), and anti-H3K27Ac (Abcam). Analyses were performed by real-time quantitative PCR. Data are represented as the ratio between the bound fraction of the HDAC7, MEF2C, and histone modification antibody relative to the input control.
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5

Chromatin Immunoprecipitation with Histone Modifications

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qChIP was performed as described33 (link) with the following modifications: 5 ml of an overnight culture grown in YPAD with extra uridine (0.08 mg/ml), diluted into fresh YPAD with extra uridine (0.08 mg/ml) and grown until OD600 nm of 1.4. Cells (50 ml/sample) were fixed with 1% Paraformaldehyde (Sigma) for 15 min at room temperature. Cells were lysed using acid-washed glass beads (Sigma) and a Disruptor genieTM (Scientific Industries) for 30 min at 4 °C. Chromatin was sheared to 500–1000 bp using a Bioruptor (Diagenode) for a total of 20 min (30 s ON and OFF cycle) at 4 °C. Immunoprecipitation was performed overnight at 4 °C using 2 μL of antibody anti-H3K4me2 (Active Motif- Cat Number: 39141), anti-H3K9ac (Active Motif- Cat Number: 39137), and anti-H4K16ac (Active Motif- Cat Number: 39167) and 25 μl of Protein G magnetic beads (Dynal - InVitrogen). DNA was eluted with a 10% slurry of Chelex 100-resin (Bio-Rad) using the manufacturer’s instructions.
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