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5 protocols using anti trimethyl histone h3k4

1

ChIP-qPCR Analysis of Epigenetic Marks

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ChIP assays were carried out as previously described using 150 µg of chromatin for EZH2 and MyoD, and 50 µg of chromatin for modified histones. In brief, chromatins were immunoprecipitated with anti-MyoD antibody ([sc-760] Santa Cruz Biotechnology), anti-EZH2 antibody (39901, Active Motif), anti trimethyl-histone H3K27 (07-449, Millipore), anti trimethyl-histone H3K4 (07-473, Millipore), normal rabbit (Millipore, 12-370) or normal mouse IgG (Millipore, 12-371). qPCR analysis was performed in triplicate for each of three independent experiments, using 5 ng of DNA, Go Taq qPCR Master Mix (Promega) and the following primer pairs:p57 prom

F: 5′5′ACTGAGAGC-AAGCGAACAGG-3′

R: 5′ACCTGGCTGATTGGTGATGG-3′;

Maternal p57i

F: 5′-CAGATCTGACCTCAGACCCA-3′

R: 5′-CCTGTTCCTCGCCGTCCC-3′;

Paternal p57i

F: 5′CAGATCTGACCTCAGACCCG-3′

R: 5′-GACCTGTTCCTCGCCATCCT-3′;

β-globin prom

F: 5′-GAAGCCTGATTCCGTAGAGC-3′

R: 5′-CAACTGATCCTACCTCACCTTATATGC-3′;

β-Actin prom

F: 5′-GTGACATCCACACCCAGAGG-3′

R: 5′-GAATAGCCTCCGCCCTTG-3′;

Amylase prom

F: 5′-TCAGATGGGAGGACTGCTATTGT-3′

R: 5′-GCTCACATTCCTTGGCAATATCA-3′;

Albumin prom

F: 5′-AATCGTCTTTGAGGCACCAG-3′

R: 5′-GCTCAATCTTCCCAAACAGG-3′;

Timm prom

F: 5′-ACGGATGTGGCCCTTCTGGCT-3′

R: 5′-CCGCTGCGAAACGCCCACAA-3′;

p57i

F: 5′-AACTTCCAGCAGGATGTGCC-3′

R: 5′-CATCCACTGCAGACGACCAG-3′

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2

ChIP Assay for Histone Modifications

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ChIP assay was performed as described previously23 (link). The antibodies using in ChIP assay as follows; anti-trimethyl histone H3-K4 (Millipore), anti-acetyl histone H3-K9 (Millipore), anti-trimethyl histone H3-K27 (Millipore) and normal rabbit IgG (Santa Cruz). The specific primers used in ChIP assay are described in Supplementary Table 2.
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3

Chromatin Immunoprecipitation in Arabidopsis

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ChIP analysis was performed according to the protocols described previously by Jiang et al. [19 (link)]. The leaves from four-week-old A. thaliana plants were harvested for experiment. Anti-trimethyl-histone H3K4 and anti-acetyl-histone H4K5K8K12K16 were purchased from Millipore Corporation. The amounts of immuno-precipitated genomic DNA were determined by real-time quantitative PCR. Each assay was quantified in triplicate and normalized using EIF4A1 (AT3g13920) as an internal control. All experiments had three biological replicates.
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4

Antibody Generation and Characterization for Epigenetic Assays

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Antibodies used in ChIP assay were purchased from Santa Cruz Biotechnology: (anti-acetyl histone H4K16, sc-8662, and anti-acetyl histone H3K9/14, sc-8655), Millipore Corporation (anti-monomethyl histone H3K4 (07-436), anti-dimethyl histone H3K4 (07-030), anti-trimethyl histone H3K4 (07-473), antimonomethyl histone H3K9 (07-450), anti-dimethyl histone H3K9 (07-441), anti-trimethyl histone H3K9 (07-442), anti-monomethyl histone H4K20(07-440), anti-dimethyl histone H4K20 (07-367), anti-trimethyl histone H4K20 (07-463), and anti-histone H3 (06-755), CoREST (07-455 from upstate), HDAC1 (05-617 from upstate) and Arabidopsis anti-LSD1 (developed in our lab). Four homologues of LSD1 found in Arabidopsis thaliana (AT1g62830, AT3g10390, AT4g 16310, AT3g13682) as described in Shi et al., 2004) were aligned using ClustalW. Peptide sequences of 16-mer length were predicted using ABC predict software and AT4G16310 as input sequence. A peptide sequence conserved on the C-terminal region of the protein i.e., H2N -HAMIKGGYSRVVESLA (AT4G16310; 848-863 aa residues) was chosen for raising anti-LSD1 antibody and was synthesized and HPLC-puri ed by GL biochem (Shanghai) Ltd. Polyclonal antibodies were custom-made in rabbits (Bangalore Genei) using this synthetic peptide and were further a nity puri ed by using protein A Sepharose column (CL-4B).
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5

Gonad Dissection and Immunostaining

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Gonads were dissected on glass slide (Thermo Fisher Scientific, 1256820) in M9 buffer, mounted in 2% paraformaldehyde (Electron Microscopy Science, Nm15710) in egg buffer (25mM HEPES pH 7.5, 118mM NaCl, 48mM KCl, 2 mM CaCl2, 2mM MgCl2), and directly imaged. Epi-fluorescence and differential interference contrast (DIC) microscopy were performed using an Axio Imager M2 Microscope (Zeiss). Images were captured with an ORCA-ER digital camera (Hamamatsu) and processed using Axiovision software (Zeiss).
Immunostaining of gonads was performed essentially as described (Kim et al., parallel) .
The primary antibodies (1:100) used were anti-acetyl-histone H3K9 antibody (Abcam, ab12179), anti-di-methyl-histone H3K9 antibody (Abcam, ab1220), and anti-tri-methyl histone H3K4 (Millipore, . The secondary antibodies (1:1000) used were goat antimouse IgG (H+L) Alexa Fluor 594 (Thermo Fisher Scientific, A11005), goat anti-mouse IgG (H+L) Alexa Fluor 488 (Thermo Fisher Scientific, A11001), and goat anti-rabbit IgG(H+L) Alexa Fluor 568 (Thermo Fisher Scientific, A11011), respectively. Epifluorescence and differential interference contrast (DIC) microscopy were performed using an Axio Imager M2 Microscope (Zeiss). Images were captured with an ORCA-ER digital camera (Hamamatsu) and processed using Axiovision software (Zeiss).
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