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32 protocols using h3k4me2

1

Antibody and Inhibitor Reagents for Assays

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Rat anti-mouse F4/80 antibody was purchased from Serotec; Rat anti-mouse CD31 was purchased from Dianova (Hamburg, Germany). Anti-actin and anti-smooth muscle actin (SMA) monoclonal antibodies were purchased from Sigma (St. Louis, MO). Antibodies directed against phopsho-AMPK alpha, phospho-p38 and phospho-JNK, histone H3 and H3K4-di (H3K4me2) and -tri (H3K4Me3) methylation, H3K27 tri-methylation and acetylated H2BK5 were purchased from Cell Signaling Technology (Beverly, MA). Anti-WDR5, anti-BiP, and anti-Ly6g antibodies were purchased from Abcam (Cambridge, UK). The selective inhibitors of LSD1 (GSK-2879552), WDR5 (OICR-9429), MKL1 (CCG-203971), CXCR2 (SB 225002), p38 (SB208530), and JNK (sp600125) were purchased from ApexBio (Boston, MA) and were dissolved in DMSO as stock solutions. DMSO (Sigma D2438) was added to the cell culture medium as control. The heparanase inhibitors H1001 and PG545 were kindly provided by HepaRx Ltd (Ness-Ziona, Israel) and Zucero Therapeutics (Darra, Queensland, Australia), respectively. Mouse CXCL2/MIP-2 Quantikine ELISA kit was purchased from R&D Systems (Minneapolis, MN). The MyD88 peptide inhibitory set was purchased from Novus Biologicals (Centennial, CO). Latent heparanase was purified from medium conditioned by CHO cells overexpressing heparanase essentially as described (25 ) and was added to cell cultures at 1 μg/ml.
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2

Histone Modification Analysis by Western Blot

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After treatment, the cells were washed with PBS and lysed with radioimmunoprecipitation assay (RIPA) buffer buffer containing phosphatase and protease inhibitors. Cell lysates were resuspended in Laemmli SDS sample buffer (60 mM Tris–HCl, 1% SDS, 10% glycerol, 0.05% bromophenol blue, pH 6.8, and 2% β-mercaptoethanol) and then subjected to 10% SDS–PAGE. The gels were then transferred to polyvinylidene difluoride (PVDF) membrane for immunoblot. Membranes were then blocked in 5% non-fat skim milk for 1 h and then incubated with primary antibody at 4° overnight. Primary antibodies directed against H3K4me3 (Cat. no. 39915; Active Motif), H3K4me2 (Cat. no. 9725; Cell Signaling), H3K4me1 (Cat. no. 9723; Cell Signaling), H3K9me3 (Cat. no. 39161; Active Motif), H3K27me3 (Cat. no. 39156; Active Motif), H3K36me3 (Cat. no. 61101; Active Motif), and H3 total (Cat. no. 39763; Active Motif) were used. Membranes were then washed three times before incubating with peroxidase-conjugated secondary antibody. Protein bands were detected using a chemiluminescence kit (Millipore).
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3

Immunoblotting Analysis of Histone Modifications

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Immunoblotting analysis was performed as previously described65 (link). Cells were washed twice with ice cold PBS, and harvested in protein lysis buffer (50 mM HEPES [pH7.4], 150 mM NaCl, 1% Triton X-100, 1 mM EDTA, 1 mM EGTA, 1 mM glycerophosphate, 2.5 mM sodium pyrophosphate, 1 mM Na3VO4, 20 mM NaF, 1 mM phenylmethylsulfonyl fluoride, 1 mM DTT, 1× complete protease inhibitor tablet [Roche]). Total cell lysates were separated on 4-12% Bis-Tris gels (Life Technologies), transferred onto PVDF membrane (Merck Millipore). The blots were probed with antibodies for H3, H3K4me2, H3K9me2, H3K27me2 (#9847 from Cell Signaling Technologies for above antibodies; 1:1000), H3K27me3 (Cell Signaling Technologies; #9733, 1:1000), SUZ12 (Cell Signaling Technologies; #3737, 1:1000), Ezh2 (Cell Signaling Technologies; #5246, 1:1000), RpAb46/48 (Santa Cruz Biotechnology; #33170, 1:1000), EED (Santa Cruz Biotechnology; #28701, 1:1000), p-S6K (Thr389, Cell Signaling Technologies; #9234, 1:1000) and S6K (Cell Signaling Technologies, MA, USA; #9202, 1:1000) as indicated in figures. Protein signals were detected using HRP conjugated secondary antibodies and enhanced chemiluminescence (ECL) western blotting detection regents (Thermo Fisher Scientific, MA, USA).
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4

Comprehensive Protein Analysis of HASMC

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Total proteins in human aortic smooth muscle cell (HASMC) and aortic tissues were extracted by RIPA solution with phosphatase inhibitors and protease inhibitors, and western blot was performed as described previously (3 (link), 16 (link), 17 (link)). The antibodies used in this study included α-SMA (ab7817), LOX (ab174316), SM22 (ab14106), H3K4me1 (ab8895), H3K36me3 (ab9050), Bax (ab32503), and Bcl-2 (ab182858) which were bought from Abcam. LOXL1 (A10191) and LOXL4 (A13131) were got from ABclonal. LOXL2 (GTX105085), MMP2 (GTX634832), MMP9 (GTX100458), H3K9me3 (GTX121677), and PCNA (GTX100539) were purchased from GeneTex. LOXL3 (sc-377216) was obtained from Santa Cruz. β-actin (#8457S), Beclin-1 (#3495), S6 (#2317), phosphorylation of S6 (p-S6) (#5364), AKT (#4685), phosphorylation of AKT (p-AKT) (#4060), p38 (#8690), p-p38 (#4511), p-JNK1/2 (#9255), p-ERK1/2 (#4370), p-GSK3 β (#5558), H3K4me2 (#9725), H3K4me3 (#9727), p-p65 (#3033), cyclinD1 (#2978), and LC3 (#12741) were purchased from Cell Signaling Technology.
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5

Immunoblot Analysis of Cellular Proteins

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Cells or tissues were lysed in modified lysis buffer (50 mM Tris-HCl, pH 7.5, 150 mM NaCl, 1 mM β-mercaptoethanol, 1% Igepal, and protease inhibitor cocktail) for 30 min on ice, followed by centrifugation at 13,000 g for 15 min at 4 °C. Equal amounts of lysates were fractionated by SDS-PAGE and subjected to immunoblot assays with the following antibodies: GPT2 (Proteintech, Rosemont, IL, USA, Cat.#: 16757-1-AP), FLAG (Sigma, St. Louis, MO, USA, Cat#: F3165), HIF-1α (homemade or BD Biosciences, San Jose, CA, USA Cat.#: 610958), HIF-2α (homemade or Novus Biologicals, Littleton, CO, USA, Cat.#: NB100-122), α-Tubulin (Santa Cruz Biotechnology, Dallas, TX, USA, Cat.#: sc-8035), Tom20 (Proteintech, Rosemont, IL, USA, Cat.#: 11802-1-AP), histone H3 (Novus Biologicals, Littleton, CO, USA, Cat.#: NB500-267), H3K9me3 (Abcam, Waltham, MA, USA, Cat.#: ab8898), H3K9me2 (Cell Signaling Technology, Danvers, MA, USA, Cat.#: 4658S), H3K9me (Sigma, St. Louis, MO, USA, Cat.#: 07-450), H3K4me3 (Sigma, St. Louis, MO, USA, Cat.#: 07-473), H3K4me2 (Cell Signaling Technology, Danvers, MA, USA, Cat.#: 9725S), H3K4me (Cell Signaling Technology, Danvers, MA, USA, Cat.#: 5326S), ITGA6 (Cell Signaling Technology, Danvers, MA, USA, Cat.#: 3750S), or actin (Proteintech, Rosemont, IL, USA, Cat.#: 66009-1-Ig).
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6

Comprehensive Antibody Validation for Cell Biology

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The antibodies used in this study included α-SMA (ab7817), SM22α (ab14106), H3K9me1 (ab9045), H3K9me2 (ab1220), H3K4me1 (ab8895), H3K36me2 (ab9049), H3K36me3 (ab9050), which were bought from Abcam. β-actin (AC026) and RAB7 (A12308) were got from ABclonal. H3K9me3 (GTX121677), MMP2 (GTX634832), MYH10 (GTX634160), MMP9 (GTX100458), PCNA (GTX100539) were purchased from GeneTex. P-H3 (sc-8656-R) was obtained from Santa Cruz. LAMP3 (AP1827A) was bought from Abgent. STX17 (HPA001204) was got from ATLAS. H3K4me2 (#9725), H3K4me3 (#9727), H3K36me1 (#14,111), p-AKT (#4060), AKT (#4685), p-FOXO3 (#9466), FOXO3A (#12,829), p-P38 (#4511), P38(#8690), p-CDC2 (#4539), p-Rb (#8516), Rb (#9313), p-CHK1(#2348), P-CHK2 (#2197), LC3A/B (#12,741), SQSTM1 (#88,588), p-AMPKα (#5831), AMPKα (#2535), p-mTOR (#5536), mTOR (#2983), LAMP1 (#9091), and COL1A1 (#91,144) were purchased from Cell Signaling Technology.
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7

Chromatin Modification and Cell Signaling Assay

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Cell Signaling antibodies (Danvers, MA): H3K9ac (Cat# 9649), H3K18ac (Cat# 9675), H3K27ac (Cat# 4353), H3K4me2 (Cat# 9725), H3K9me2 (Cat# 4658), H3K27me3 (Cat# 9733), Histone H3 (Cat# 4499), GAPDH (Cat# 5174), cleaved caspase-3 (Cat# 9661), HRP-linked anti-rabbit IgG (Cat# 7074) and HRP-linked anti-mouse IgG (Cat# 7076). DAKO (Glostrup, Denmark) antibodies: Ki-67 (Cat# M7240) and ACTH (Cat# N1531). Chemicon International antibodies (Temecula, CA): GLUT-1 (Cat# AB1341). Abcam (Cambridge, UK) antibodies: TPIT (Cat# ab243028) and SF1 (Cat# ab168380). Santa Cruz (Dallas, TX) antibodies: PIT1 (Cat# sc-393943). Reagents used are sodium acetate (Sigma-Aldrich, St. Louis, MO; Cat# S5636), PP242 (Cayman Chemical, Ann Arbor, MI, Cat# 13643), BPTES (Selleck, Houston, TX, Cat# S7753), 2-Deoxy-D-Glucose (2-DG) (FUJIFILM Wako, Osaka, Japan, Cat# 040-06481) and L1H1-7OTD (Cosmo Bio, Tokyo, Japan, Cat# TAT-004). Information on antibodies used in the study was summarized in Table 1.
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8

Antibodies for Protein Analysis Techniques

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The following primary antibodies were used in western blotting assays: NPM1 mutant (NB110-61646, Novus, Littleton, USA), NPM1 WT (Thermo scientific, Rockford, USA), NPM1 (Sigma-Aldrich, St. Louis, USA), PBX3 (Abcam, Cambridge, USA), HOXA9 (Abcam, Cambridge, USA), Cleaved caspase 3, Cleaved PARP (Cell Signaling, Danvers, USA), Flag, H3K4me2, H3K9me2, H3K27me2, H3K36me2, H3K79me1, H3K79me2, H3K79me3, H3, DOT1L (Cell Signaling, Danvers, USA), and β-Actin (Sigma, St. Louis, MO, USA).
All antibodies and the following kits applied in flow cytometry analyses were purchased from BD Biosciences (BD Pharmingen™, New Jersey, USA): CD45.1, CD45.2, Mac-1, Gr-1, Sca-1, c-Kit, Mouse Lineage Panel, AnnexinV Apoptosis Detection kit, and BrdU Flow kit.
Immunofluorescence staining was performed with Flag (Cell Signaling, Danvers, USA), H3K79me2 (Cell Signaling, Danvers, USA and PMT-bio, Hangzhou, China), PBX3 (Santa Cruz, California, USA), HOXA9 (Abcam, Cambridge, USA) and NPM1 antibodies as following: NPM1 mutant (Novus, Littleton, USA), NPM1 WT (Thermo scientific, Rockford, USA), NPM1 (Cell Signaling, Danvers, USA).
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9

Biotinylated Peptide Synthesis and Analysis

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Biotinylated peptides were synthesized at the UNC High-Throughput
Peptide Synthesis and Array Facility (Chapel Hill, NC)22 (link). Fmoc-L-histidine amino acids with
either (1-me) or (3-me) modifications (Sigma-Aldrich) were used in the synthesis
of these peptides and synthesized peptides were purified by HPLC (>92%
purity). Antibodies used in this study: SETD3 (Abcam), pan-actin (Cytoskeleton),
beta-tubulin (Millipore), H3K4me2 (Cell Signaling), H3K36me2 (Cell Signaling),
H73(3-me) see below, GFP (Invitrogen), Alexa488 anti-rabbit antibody (Life
Technologies), anti-rabbit and anti-mouse peroxidase conjugated antibodies
(Jackson Immunoresearch). Western blots were visualized by chemiluminescence (GE
Healthcare).
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10

Chromatin Immunoprecipitation Protocol for Epigenetic Markers

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ChIP assays were performed using the MagnaChIP Kit (Millipore) following the manufacturer's protocol. Cells were cross-linked with 1% formaldehyde, lysed and sonicated to acquire the DNA fragments of 200-500 bp. Then, the chromatin was immunoprecipitated with antibodies against EZH2, LSD1, H3K27me3, H3K4me2 or control IgG (Cell Signaling Technology). Precipitated chromatin DNA was purified and detected by qRT-PCR. The primer sequences for TFPI2 promoter region amplification are 5′-GGATGTTTGTTTTGTATAAAGTG-3′ (Forward) and 5′-AAACATCCAAAAAAACACCTAAC-3′ (Reverse). ChIP data is shown as a percentage relative to input DNA.
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