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αh3k4me3

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αH3K4me3 is a lab equipment product that detects the trimethylation of lysine 4 on histone H3 (H3K4me3). This modification is associated with active gene transcription.

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Lab products found in correlation

αcdc73, by Fortis Life Sciences (4 mentions) αh3k79me2, by Abcam (3 mentions) α h3k4me1, by Abcam (3 mentions) α gapdh, by Merck Group (2 mentions) α β actin, by Merck Group (2 mentions) αpaf1, by Fortis Life Sciences (2 mentions) αprmt5, by Merck Group (2 mentions) αsym10, by Merck Group (2 mentions) αh2bub, by Merck Group (2 mentions) αh4r3me2s, by Abcam (2 mentions) αr me2s, by Cell Signaling Technology (2 mentions) Supersignal west pico chemiluminescent substrate, by Thermo Fisher Scientific (2 mentions) Chemidoc xr, by Bio-Rad (2 mentions) α flag, by Merck Group (2 mentions) αleo1, by Fortis Life Sciences (2 mentions) Stat5 y694, by Cell Signaling Technology (2 mentions) Myc tag 71d10, by Cell Signaling Technology (2 mentions) α h3k27me3, by Merck Group (2 mentions) α h3k9ac, by Abcam (1 mentions) Ssoadvanced sybr supermix, by Bio-Rad (1 mentions)

11 protocols using αh3k4me3

1

Western Blot Analysis of Histone Modifications

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Western blots were performed with whole cell lysates or acid extracted histones and probed with the following antibodies: αCDC73, αPAF1 (Bethyl, Montgomery, TX), αPRMT5, αSYM10, αGAPDH, αH2BUb (Millipore, Billerica, MA), αH3, αH3K4me3, αH3K79me2, αH4R3me2s (Abcam,Cambridge, UK), αR-Me2s (Cell Signaling, Danvers, MA), α-βActin (Sigma). Bands were detected using SuperSignal West Pico Chemiluminescent substrate (Thermo-Fisher Scientific, Waltham, MA) and imaged on a ChemiDocXRS (Bio-Rad, Hercules, CA).
Serio J., Ropa J., Chen W., Mysliwski M., Saha N., Chen L., Wang J., Miao H., Cierpicki T., Grembecka J, & Muntean A.G. (2017). The PAF Complex Regulation of Prmt5 Facilitates the Progression and Maintenance of MLL-Fusion Leukemia. Oncogene, 37(4), 450-460.
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2

Chromatin Immunoprecipitation in Paramecium

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Chromatin isolation, sonication, fixation and immunoprecipitation were carried out as described previously using shearing fragments of 300–500 bp (41 (link)). The antibodies used were αH3 and H3K27me3 (07-442 and 07-449; Merck-Millipore, Darmstadt, Germany), and αH3K9ac and αH3K4me3 (ab4441 and ab8580; Abcam, Cambridge, UK). The H3K27me3 antibody has been shown to specifically detect this modification in Paramecium histone H3 in spite of one amino acid mismatch to the immunogen peptide (42 (link)). Immunogenic peptides of the remaining antibodies fit 100% to Paramecium histone H3. DNA quantification of ChIP eluates was carried out by qPCR with the SsoAdvanced™ SYBR®Supermix (BioRad, Munich, Germany). All ChIPs were carried out in biological triplices, thus three cultures (wild type or feeding) of the same transgenic line with one ChIP per antibody each and three technical PCR replicates each.
Götz U., Marker S., Cheaib M., Andresen K., Shrestha S., Durai D.A., Nordström K.J., Schulz M.H, & Simon M. (2016). Two sets of RNAi components are required for heterochromatin formation in trans triggered by truncated transgenes. Nucleic Acids Research, 44(12), 5908-5923.
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3

Chromatin Regulation Antibody Panel

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The following antibodies were used: αAurura B (AIM1) (Cell Signalling, 3094), αBmi1 (Cell Signalling, 6964), αBRD4 (Cell Signalling, 12183), αCTCF (Cell Signalling, 3418), αCyclinB (Cell Signalling, 4138), αDNMT1 (Abcam, ab92453), αH2AK119Ub (Cell Signalling, 8240), αH2BK120Ub (Cell Signalling, 5546), αH3 (Abcam, ab1791 and Cell Signalling, 4620), αH3K4me3 (Abcam, ab8580), αH3K9ac (Cell Signalling, 9649), αH3K9me2/3 (Cell Signalling, 5327), αH3S10ph (Sigma, H 0412), αH4 (Abcam, ab31830), αHP1α (Cell Signaling, 2616), αphosphoSer2-PolII (Covance, MMS-129R), αRunx2 (Cell Signalling, 8486), and αTBP (Abcam, ab62125).
Halley-Stott R.P., Jullien J., Pasque V, & Gurdon J. (2014). Mitosis Gives a Brief Window of Opportunity for a Change in Gene Transcription. PLoS Biology, 12(7), e1001914.
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4

Genome-wide Histone Modification Analysis in S. cerevisiae

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The S. cerevisiae strain used in this study for the genome-wide location analysis was BY4742, derived from S288C.
The experiments described in this study compared ChIP with a histone modification antibody to a control ChIP with a core histone antibody. The antibodies (obtained from rabbit, ChIP Grade) recognizing the histone modifications were: α-H3K9ac (Upstate, 06–942), α-H3K14ac (Upstate, 07–353), α-H3K4me1 (Abcam, 8895), α-H3K4me3 (Abcam, 8580), α-H3K36me3 (Abcam, 9050), α-H3K79me2 (Abcam, 3594), α-H3K79me3 (Abcam, 2621), and α-H4K8ac (Abcam, 15823). The antibodies used in the control channel in the ChIP-Chip procedure were α-H3 (Abcam, 1791) for the modifications of the histone H3 experiments and α-H4 (Abcam, 10158) for the modifications of the histone H4 experiments.
Magraner-Pardo L., Pelechano V., Coloma M.D, & Tordera V. (2014). Dynamic remodeling of histone modifications in response to osmotic stress in Saccharomyces cerevisiae. BMC Genomics, 15(1), 247.
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5

ChIP-qPCR Protocol for Chromatin Analysis

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ChIP-qPCR was performed as described64 (link), using αCDC73, αLEO1 (Bethyl, Montgomery, TX), αMLLc (gift from Dr. Yali Dou), αFlag (Sigma), αH3K4me3, αH3 (Abcam, Cambridge, UK), IgG (Santa Cruz, Dallas, TX), Stat5-Y694 and Myc-Tag-71D10 (Cell Signaling, Danvers, MA). qPCR primer sequences are listed (Table S1).
Serio J., Ropa J., Chen W., Mysliwski M., Saha N., Chen L., Wang J., Miao H., Cierpicki T., Grembecka J, & Muntean A.G. (2017). The PAF Complex Regulation of Prmt5 Facilitates the Progression and Maintenance of MLL-Fusion Leukemia. Oncogene, 37(4), 450-460.
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6

Chromatin Immunoprecipitation Antibodies

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ChIP-grade antibodies were αH3.3K27me3 (custom antibody made by Proteintech), αH3.3 (Invitrogen RM190), αH3K27me3 (Active Motif 39155), αH3 (Abcam 1791), rabbit IgG (Abcam 171870) (Fig. S5). Additional antibodies used for western blotting (WB) included αH3K27me3 (Abcam 6002), αREST (EMD Millipore 07–579), αH3K4me3 (Abcam 8580), αH3K27ac (Active Motif 39133), and αH3K9me3 (Abcam 8898).
Kori Y., Lund P.J., Trovato M., Sidoli S., Yuan Z.F., Noh K.M, & Garcia B.A. (2022). Multi-omic profiling of histone variant H3.3 lysine 27 methylation reveals a distinct role from canonical H3 in stem cell differentiation. Molecular omics, 18(4), 296-314.
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7

Western Blot Analysis of Histone Modifications

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Western blots were performed with whole cell lysates or acid extracted histones and probed with the following antibodies: αCDC73, αPAF1 (Bethyl, Montgomery, TX), αPRMT5, αSYM10, αGAPDH, αH2BUb (Millipore, Billerica, MA), αH3, αH3K4me3, αH3K79me2, αH4R3me2s (Abcam,Cambridge, UK), αR-Me2s (Cell Signaling, Danvers, MA), α-βActin (Sigma). Bands were detected using SuperSignal West Pico Chemiluminescent substrate (Thermo-Fisher Scientific, Waltham, MA) and imaged on a ChemiDocXRS (Bio-Rad, Hercules, CA).
Serio J., Ropa J., Chen W., Mysliwski M., Saha N., Chen L., Wang J., Miao H., Cierpicki T., Grembecka J, & Muntean A.G. (2017). The PAF Complex Regulation of Prmt5 Facilitates the Progression and Maintenance of MLL-Fusion Leukemia. Oncogene, 37(4), 450-460.
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8

ChIP-qPCR Protocol for Chromatin Analysis

Cited 1 time
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ChIP-qPCR was performed as described64 (link), using αCDC73, αLEO1 (Bethyl, Montgomery, TX), αMLLc (gift from Dr. Yali Dou), αFlag (Sigma), αH3K4me3, αH3 (Abcam, Cambridge, UK), IgG (Santa Cruz, Dallas, TX), Stat5-Y694 and Myc-Tag-71D10 (Cell Signaling, Danvers, MA). qPCR primer sequences are listed (Table S1).
Serio J., Ropa J., Chen W., Mysliwski M., Saha N., Chen L., Wang J., Miao H., Cierpicki T., Grembecka J, & Muntean A.G. (2017). The PAF Complex Regulation of Prmt5 Facilitates the Progression and Maintenance of MLL-Fusion Leukemia. Oncogene, 37(4), 450-460.
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9

Chromatin Modification and Transcription Analysis

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α-H3K4me3 (Abcam[UK]-8580), α-H3K4me1(Abcam-8895), α-H3K27me3 (Millipore[UK]-07-449), α-H3K9/K14ac (Abcam 12,179), α-H3 (Abcam 1791), α-SUZ12 (Abcam 12,073-100), α-RNA Pol II N20 (Santa-Cruz[UK] 899), α-RNA Pol II S5P (Abcam 5131), α-RNA Pol II unphosphorylated CTD (Abcam 817), α-GFP (Chromotec [Germany] GFP-TRAP-A gta-20), α-IgG (Invitrogen 10500C).
Wachter E., Quante T., Merusi C., Arczewska A., Stewart F., Webb S, & Bird A. (2014). Synthetic CpG islands reveal DNA sequence determinants of chromatin structure. eLife, 3, e03397.
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10

Probing Histone H3 Modifications Dynamics

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Protein extracts were prepared from vegetative, pre-meiotic, or meiotic cultures as described previously (Cooper et al. 1997 (link)). Either 100 or 25 µg of whole-cell protein extract was used for α-myc-Set1 or histone H3 modifications, respectively. Following transfer onto PVDF, membranes were incubated with α-H3 C-terminal domain (1:5000; Abcam ab1791), α-H3K4me1 (1:2500; Abcam ab8895), α-H3K4me2 (1:2500; Abcam ab11946), or α-H3K4me3 (1:2500; Abcam ab8580). Myc-epitope tagged Set1 protein levels were monitored using α-myc (1:3000; Abcam ab32) with α-alpha Tubulin (1:5000; Abcam ab184970) or α-Pgk1 (1:5000; Abcam ab113687) serving as a loading control. Secondary antibodies were conjugated with alkaline phosphatase (1:5000; α-mouse Abcam ab6790; α-rabbit Abcam ab97097) and signal was detected using CDP star detection reagent.
Trainor B.M., Ciccaglione K., Czymek M, & Law M.J. (2021). Distinct requirements for the COMPASS core subunits Set1, Swd1, and Swd3 during meiosis in the budding yeast Saccharomyces cerevisiae. G3: Genes|Genomes|Genetics, 11(11), jkab283.
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