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6 protocols using anti h4k5ac

1

Histone Acetylation Analysis Protocol

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The ground fine powder of each time point was mixed with extraction buffer containing 100 mM Tris, pH 8.0, 1.5 M β-mercaptoethanol, 4% SDS, 15% glycerol, 2 mM EDTA, 0.005% bromophenol blue, 2 μM/mL Trichostatin A (TSA) and vortexed for 30 s. The mixed solution was boiled for 5 min at 99 °C and vortexed 30 s. The supernatants were transferred into a new collection tube after centrifugation at 15,000 g for 10 min at RT. Proteins were loaded into 12% sodium dodecylsulfate-polyacryamide gel electrophoresis (SDS-PAGE) for protein separation and transferred to a polyvinylidene fluoride (PVDF) membrane, and probed using anti-H3 (ab1791) and anti-H3K18ac (ab1191) from Abcam, anti-H3K23ac (#07–355), anti-H3AC (#06–599), anti-H4K5ac (#07–327), anti-H4K8ac (#07–328), anti-H4K12ac (#07–595) and anti-H4K16ac (#07–329) from Millipore at a dilution of 1:2000 (v/v) in 5% skim-milk TBST (10 mM Tris-HCl, pH 75, 150 mM NaCl, and 0.1% Tween 20) for 1 h at RT after incubation with blocking buffer for 1 h at RT. The membranes were washed three times with TBST for 5 min each. Next, membranes were incubated with secondary antibody (AS014, ABclonal, Inc) in 5% skim-milk-TBST for 1 h at RT. Signals in membranes were detected using the BLT Gel View 6000 Plus machine (Biolight Biotec Co., Ltd.).
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2

Profiling Histone Modifications and Neuronal Markers

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Antibodies included Anti-H3 (Abcam ab1791), Anti-H3K9ac (Abcam ab4441), Anti-H3K27ac (Abcam ab4729), Anti-H3K122ac (Abcam ab33308), Anti-H4 (Millipore 05-858), Anti-H4K5ac (Millipore 39-584), Anti-H4K12ac (Abcam ab1761), Anti-ACSS2 (T) (Thermo MA5-145810), Anti-ACSS2 (CS) (Cell Signaling 3658), Anti-ACL (Proteintech 15421-1-AP), Anti-α-Tubulin (Sigma T8328), Anti-GAPDH (Fitzgerald Industries 10R-G109A), Anti-KAT3A/CBP (Abcam ab2832), Anti-SNAP25 (Abcam ab5666), Anti-Synaptophysin (Millipore MAB368), Anti-MAP2 C/D (Cell Signaling #8707), Anti-NR4A2 (Santa Cruz sc-991), Anti-NeuN (Millipore ABN78)
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3

In vitro Histone Acetyltransferase Activity Assay

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For in vitro histone acetyltransferase activity assay, vectors of HAG704, ACLA2, ACLB-3×FLAG, and H4-6×His were transformed into tobacco (Nicotiana benthamiana) leaf epidermal cells. 48 h after the transfection, the transfected tobacco leaves were collected and ground into powder by liquid nitrogen. Then the proteins were extracted with lysis buffer (10 mM Tris-HCl pH 7.5, 150 mM NaCl, 0.5 mM EDTA, 0.5% Nonidet™ P40 Substitute) and purified with Ni-NTA Magnetic Agarose beads (QIAGEN, 36113). The extracted proteins were boiled at 90 °C for 10 min and then analyzed using Western blotting. The primary antibodies used were anti-HAG704 (1:1000, in house), anti-H3 (1:1000, Abcam, ab1791), anti-H3K9ac (1:1000, Millipore, 07–352), anti-H3Kac (1:1000, Millipore, 17-615), anti-H4 (1:1000, Abcam, ab177840), anti-H4K12ac (1:1000, PTM-Biolab, PTM-121), anti-H4K5ac (1:1000, Millipore, 07-327), anti-H4K16ac (1:1000, Millipore, 07-329), anti-ACLA2 (1:1000, homemade), anti-FLAG (1:1000, Sigma, F3165). The secondary antibodies used were peroxidase-conjugated goat anti-rabbit antibody (1:10000, Abbkine, A21020), and peroxidase-conjugated goat anti-mouse antibody (1:10000, Abbkine, A21010). The original raw blotting images are shown as a Source Data file.
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4

Profiling Histone Modifications and Neuronal Markers

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Antibodies included Anti-H3 (Abcam ab1791), Anti-H3K9ac (Abcam ab4441), Anti-H3K27ac (Abcam ab4729), Anti-H3K122ac (Abcam ab33308), Anti-H4 (Millipore 05-858), Anti-H4K5ac (Millipore 39-584), Anti-H4K12ac (Abcam ab1761), Anti-ACSS2 (T) (Thermo MA5-145810), Anti-ACSS2 (CS) (Cell Signaling 3658), Anti-ACL (Proteintech 15421-1-AP), Anti-α-Tubulin (Sigma T8328), Anti-GAPDH (Fitzgerald Industries 10R-G109A), Anti-KAT3A/CBP (Abcam ab2832), Anti-SNAP25 (Abcam ab5666), Anti-Synaptophysin (Millipore MAB368), Anti-MAP2 C/D (Cell Signaling #8707), Anti-NR4A2 (Santa Cruz sc-991), Anti-NeuN (Millipore ABN78)
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5

Chromatin Immunoprecipitation Protocol for Rice

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0.5–1 g of rice seeds (3 DAF) or leaves (30-day-old) was vacuum-crosslinked in 1% formaldehyde. Ultrasound fragmented chromatin to 200–800 bp. 5 µL anti-H4K5ac (Millipore, 07-327) or anti-HAG704 and 40 µL protein A beads (Invitrogen, 88845) were incubated at 4 °C for more than 4 h. About 100 µL fragmented chromatin suspension was added after bead washing, then incubated overnight at 4 °C. After washing, reverse cross-linked immunoprecipitated chromatin was used for qPCR. ChIP-qPCR primers were listed in Supplementary Data 5. Three biological replicates were performed using samples collected from three independent cultures.
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6

Histone Modification Analysis in Poplar

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Total proteins from leaves, Sc, Sv, and roots of control and TSA-treated poplar were extracted using a phenol (Sigma, St. Louis, MO, United States) extraction procedure as described previously (Hurkman and Tanaka, 1986 (link); Wang et al., 2011 (link)). Protein concentrations were measured using the Bio-Rad Protein Assay (Bio-Rad, United States). Thirty micrograms of protein was separated by 15% SDS-PAGE gel and transferred by electroblotting (180 mA for 3 h) to a PVDF membrane (Millipore, Billerica, MA, United States). Membranes were blocked with 5% skim milk and probed with anti-H3K9ac (07-352, Millipore, Billerica, MA, United States) and anti-H4K5ac (07-327, Millipore, Billerica, MA, United States) antibodies to detect histone marks. Polyclonal anti-actin (EASYBIO, Beijing, China) antibody was used as a control for protein loading. Fluorescence goat anti-rabbit (GAR) antibody (Odyssey, United States) was used as the secondary antibody. Membranes were digitized using a two-photo far infrared scanner (Odyssey, United States) and analyzed with Image Studio software4. Western blotting experiments were repeated three times for each protein sample.
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