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11 protocols using anti h4

1

Histone Hyperacetylation Assessment in Plants

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Total protein extraction from plants and protein gel blot analysis refer to the described method (Xiao et al., 2013 (link)). The histone-rich proteins were separated by 15% SDS-PAGE. Then, the proteins were transferred to the polyvinylidene fluoride (Biotrace TM, USA) membrane, blocked with 5% skimmed milk powder in TBST, and then treated with Anti-H4ace [H4 hyperacetylation (K5K8K12K16)] (1:10,000; Millipore, Anti-H4ace: 06598) to detect. Anti-H4 (1:10,000; Millipore, Anti-H4: 07-108) was a loading control.
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2

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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3

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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4

Affinity Purification of Recombinant Proteins

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The recombinant plasmids pET28a-His-CAPG and pGEX-4T-1-GST-PRMT5 were individually transformed into BL21(DE3) cells and incubated for 16 h on LB agar plates at 37 °C. Selected colonies were extracted and cultured in LB medium, followed by induction with 0.1 mM IPTG upon reaching an OD at 600 nm of 0.4. The transformed E. coli were lysed via sonication (VCX130/VCX130PB, Sonics & Materials, Inc., USA). The supernatant was collected after centrifugation at 10,000 ×g at 4 °C for 20 min. The supernatant was also passed through a Ni-NTA His-tag high-performance nickel-Sepharose column (GE Healthcare, Sweden). The GST and GST-tagged proteins were purified from bacterial lysates using glutathione-agarose beads (Amersham Biosciences). Purified core histone protein was purchased from Millipore (Millipore, Merck KGaA, Darmstadt, Germany).
Protein immunoprecipitation, GST pull-downs, and Western blotting were performed as described previously 57 (link), 60 (link), 61 (link). The following antibodies were used: anti-CAPG, anti-STC-1 (Santa Cruz Biotechnology, Inc., USA); mouse anti-FLAG (Sigma-Aldrich, USA); anti-PRMT5, rabbit anti-HA, mouse anti-HA, anti-His, rabbit anti-FLAG, anti-H3R8me2s, and anti-H4R3me2s (Abcam Inc., USA); anti-H4 (Millipore, Germany); and anti-GAPDH (ProteinTech Group, USA).
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5

Methylation Analysis of Histone and ERF1

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His‐tagged ERF1‐WT/Q185K and GST‐tagged H4 WT/K12Q proteins or recombinant nucleosomes were incubated with HEMK2/TRMT112 or SETD6 in methylation buffer supplemented with 0.76 μM labeled [methyl‐3H]‐AdoMet (Perkin Elmer) at 25°C. Concentrations and methylation times are stated in the text. The methylation reactions were stopped by the addition of SDS loading buffer and boiling for 5 min at 95°C. Equal loading of target protein amounts was confirmed by Coomassie Brilliant Blue staining and Western Blot using as primary antibody anti‐H4 (Millipore, 05‐858, Lot: 3768156) for GST‐tagged H4 or anti‐His (Qiagen, Hilden, Germany) for His‐tagged ERF1. The methylated protein samples were separated by 16% SDS‐PAGE, whereas methylated nucleosome samples were separated by tricine gel electrophoresis. Then, the gels were incubated for 1 h in Amplify NAMP 100 V (GE Healthcare) and dried for 90 min at 70°C under vacuum. The dried gels were exposed to Hyperfilm™ high‐performance autoradiography films (GE Healthcare) in the dark at −80°C. Film development was performed with an Optimus TR developing machine.
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6

Antibody Sources and Applications

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Antibodies used in this study and their sources are as follows: anti-TRPS1 (R&D Systems#AF4838), anti-HDAC2 (Cell Signaling Technology#5113), anti-H4K16ac (Millipore#39929), anti-H4 (Millipore#04–858), anti-USP4 (Cell Signaling Technology#2651), anti-actin (proteintech#60008–1-Ig), anti-HA (Biotool#B23402), anti-Flag (Sigma#F7425), anti-Myc (Biotool#B23402), anti-His (Cell Signaling Technology#12698), and anti-Gal4 (Santa Cruz#510).
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7

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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8

Western Blot Protein Analysis

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Total cell extracts were prepared using the TCA method (Keogh et al., 2006 (link)). Proteins were separated on 8–15% SDS-PAGE gels and transferred to polyvinylidene fluoride (PVDF) membranes (Millipore, Billerica, MA). The membranes were probed with specific antibodies, and immuno-reactivity was detected using enhanced chemiluminescence reagent (Elpis Biotech, Korea). The primary antibodies were anti-Sir2 (1:200, Santa Cruz, Dallas, TX), anti-FLAG (1:1000, Sigma, Saint Louis, MO), anti-Myc (1:1000, Santa Cruz), anti-GAPDH (1:10,000, Acris, Germany), anti-AcH4K16 (1:2000, Upstate, Lake Placid, NY), and anti-H4 (1:0000, Millipore). Band density trace and quantification were determined using ImageJ (National Institutes of Health).
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9

Antibody-based Protein Detection

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Anti-FLAG antibody (Sigma-Aldrich, A8592), anti-GFP antibody (Roche, 11,814,460,001), anti-GAPDH antibody (Ambion, AM4300), anti-H4 (Millipore, 07-108) and oligos (Sigma-Aldrich) were used.
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10

Antibody Characterization for Histone Regulation

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The following antibodies were used in this study: anti-HIRA (Active Motif, Carlsbad, CA, USA, WC119 and WC15), anti-Asf1a (Cell Signaling, Danvers, MA, USA, 2990), anti-Cabin1, anti-UBN1 (Abcam, Cambridge, MA, USA), anti-H3 (Abcam, ab1791), anti-H4 (Millipore, Billerica, MA, USA, 07–108), anti- H4S47p (Abcam), anti-H3.3 (Millipore, 09–838), anti-H3.1 and anti-H3.3 (provided by Dr Y Ohkawa), anti-pan-Akt, anti-Akt1, anti-Akt2, anti-p-Akt (S473) (Cell Signaling, 9271), anti-phospho-serine (Abcam, ab9332), anti-phospho-threonine (Abcam, ab9337), anti-myogenin (Santa Cruz, Santa Cruz, CA, USA, sc-576), anti-MHC (Upstate, Billerica, MA, USA, 05–716), 8WG16 (Covance, Princeton, NJ, USA, MMS-126R), anti-HA (Roche, Basel, Switzerland, 11 666 606 001), anti-Flag (Sigma-Aldrich, F3165), anti-Myc (Roche, 11 667 203 001), anti-β-catenin (Santa Cruz, sc-7963), and anti-α-tubulin (AbFrontier, Seoul, Korea, LF-PA0146). The anti-p-HIRA (Abmart, Shanghai, China) antibody was generated using the phospho-peptides RPRKD(pS)RLMPV and was affinity-purified from rabbit serum using a specific column. Antibody specificity was confirmed by checking the absence of cross-reactivity with the control peptide, RPRKDSRLMPV.
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