mononucleosomes Search Results


  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 94
    EpiCypher hela mononucleosomes
    UHRF1 and UHRF2 diverge in their ability to ubiquitinate nucleosomal histones. ( A ) Chromatin association assays for FLAG-tagged UHRF2 (WT) or the indicated mutants from asynchronously growing <t>HeLa</t> cells. Mock treatment represents an empty vector control. ( B ) Comparative in vitro ubiquitination of H3 (1–32) K9me2 (left) and HeLa <t>mononucleosomes</t> (right) by UHRF1 and UHRF2. Moles of H3 are equivalent in these reactions.
    Hela Mononucleosomes, supplied by EpiCypher, used in various techniques. Bioz Stars score: 94/100, based on 52 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hela mononucleosomes/product/EpiCypher
    Average 94 stars, based on 52 article reviews
    Price from $9.99 to $1999.99
    hela mononucleosomes - by Bioz Stars, 2020-02
    94/100 stars
      Buy from Supplier

    97
    EpiCypher mononucleosomes
    Characterizing lysine prioritization of UHRF1 ubiquitylation on <t>mononucleosomes.</t> ( A ) Ubiquitylation of Hela mononucleosomes after 2 hr in the presence of HeDNA or UnDNA. ( B ) Ratio and normalized ratio (HeDNA/UnDNA) for H3 ubiquitylated peptides from propionylated samples. Samples were normalized to the mean ratio of free ubiquitin peptides. Quantification was performed with Skyline and values for each peptide charge state were summed. ( C ) Ratio and normalized ratio (HeDNA/UnDNA) for H3 ubiquitylated peptides from propionylated and unreacted samples. A ubiquitylated peptide from the PHD (marked with an asterisk) wa s enriched in the HeDNA sample. ( D ) Location of UHRF1 auto-ubiquitylation sites lining the TTD-PHD. TTD, pink; PHD, blue; modified lysines, red. The C-terminal atom on the H3 peptide (S10) is shown as a sphere. ( E ) Auto-ubiquitylation of UHRF1 in the absence of H3 peptides with either HeDNA or UnDNA when run under conditions to resolve higher molecular weight species. DOI: http://dx.doi.org/10.7554/eLife.17101.015
    Mononucleosomes, supplied by EpiCypher, used in various techniques. Bioz Stars score: 97/100, based on 24 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/mononucleosomes/product/EpiCypher
    Average 97 stars, based on 24 article reviews
    Price from $9.99 to $1999.99
    mononucleosomes - by Bioz Stars, 2020-02
    97/100 stars
      Buy from Supplier

    95
    GE Healthcare mononucleosomes
    Mononucleosome preparation from H3 D /H3 H cells. ( A ) <t>Mononucleosomes</t> were prepared from H3 D /H3 H cells, and purified by fast protein liquid chromatography. Molecular standards are labeled above the elution profile. ( B ) Fractions around the peak fractions (No. 14 to 31) were collected and denatured. The length of DNA was analyzed in a 2% agarose gel. Size markers are on the left. ( C ) Histone H3 in the fractions (labeled on top) was examined by western blotting using the anti-H3 N-terminal antibody. Fraction 26 was selected as mononucleosomes for further experiments.
    Mononucleosomes, supplied by GE Healthcare, used in various techniques. Bioz Stars score: 95/100, based on 81 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/mononucleosomes/product/GE Healthcare
    Average 95 stars, based on 81 article reviews
    Price from $9.99 to $1999.99
    mononucleosomes - by Bioz Stars, 2020-02
    95/100 stars
      Buy from Supplier

    87
    Helicos mononucleosomes
    Mononucleosome preparation from H3 D /H3 H cells. ( A ) <t>Mononucleosomes</t> were prepared from H3 D /H3 H cells, and purified by fast protein liquid chromatography. Molecular standards are labeled above the elution profile. ( B ) Fractions around the peak fractions (No. 14 to 31) were collected and denatured. The length of DNA was analyzed in a 2% agarose gel. Size markers are on the left. ( C ) Histone H3 in the fractions (labeled on top) was examined by western blotting using the anti-H3 N-terminal antibody. Fraction 26 was selected as mononucleosomes for further experiments.
    Mononucleosomes, supplied by Helicos, used in various techniques. Bioz Stars score: 87/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/mononucleosomes/product/Helicos
    Average 87 stars, based on 7 article reviews
    Price from $9.99 to $1999.99
    mononucleosomes - by Bioz Stars, 2020-02
    87/100 stars
      Buy from Supplier

    81
    EpiCypher biotinylated mononucleosomes
    Mononucleosome preparation from H3 D /H3 H cells. ( A ) <t>Mononucleosomes</t> were prepared from H3 D /H3 H cells, and purified by fast protein liquid chromatography. Molecular standards are labeled above the elution profile. ( B ) Fractions around the peak fractions (No. 14 to 31) were collected and denatured. The length of DNA was analyzed in a 2% agarose gel. Size markers are on the left. ( C ) Histone H3 in the fractions (labeled on top) was examined by western blotting using the anti-H3 N-terminal antibody. Fraction 26 was selected as mononucleosomes for further experiments.
    Biotinylated Mononucleosomes, supplied by EpiCypher, used in various techniques. Bioz Stars score: 81/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/biotinylated mononucleosomes/product/EpiCypher
    Average 81 stars, based on 4 article reviews
    Price from $9.99 to $1999.99
    biotinylated mononucleosomes - by Bioz Stars, 2020-02
    81/100 stars
      Buy from Supplier

    79
    Active Motif recombinant mononucleosomes
    Mononucleosome preparation from H3 D /H3 H cells. ( A ) <t>Mononucleosomes</t> were prepared from H3 D /H3 H cells, and purified by fast protein liquid chromatography. Molecular standards are labeled above the elution profile. ( B ) Fractions around the peak fractions (No. 14 to 31) were collected and denatured. The length of DNA was analyzed in a 2% agarose gel. Size markers are on the left. ( C ) Histone H3 in the fractions (labeled on top) was examined by western blotting using the anti-H3 N-terminal antibody. Fraction 26 was selected as mononucleosomes for further experiments.
    Recombinant Mononucleosomes, supplied by Active Motif, used in various techniques. Bioz Stars score: 79/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/recombinant mononucleosomes/product/Active Motif
    Average 79 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    recombinant mononucleosomes - by Bioz Stars, 2020-02
    79/100 stars
      Buy from Supplier

    77
    Illumina Inc mononucleosome cores
    Number of binding sites identified in treatment and control sample using different sets of parameters . (A - C) Box-plots show the ratios of predicted binding site counts in treatment and control achieved with different parameter choices. Lower values suggest higher specificity. (D) The number of predicted nucleosomes in the control sample is plotted versus the number of nucleosomes identified from the <t>mononucleosome</t> sample. Different colours correspond to different background rate cut-offs while different symbols indicate different cut-off levels for support region rates.
    Mononucleosome Cores, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 77/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/mononucleosome cores/product/Illumina Inc
    Average 77 stars, based on 5 article reviews
    Price from $9.99 to $1999.99
    mononucleosome cores - by Bioz Stars, 2020-02
    77/100 stars
      Buy from Supplier

    83
    EpiCypher cenp a mononucleosome
    Number of binding sites identified in treatment and control sample using different sets of parameters . (A - C) Box-plots show the ratios of predicted binding site counts in treatment and control achieved with different parameter choices. Lower values suggest higher specificity. (D) The number of predicted nucleosomes in the control sample is plotted versus the number of nucleosomes identified from the <t>mononucleosome</t> sample. Different colours correspond to different background rate cut-offs while different symbols indicate different cut-off levels for support region rates.
    Cenp A Mononucleosome, supplied by EpiCypher, used in various techniques. Bioz Stars score: 83/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/cenp a mononucleosome/product/EpiCypher
    Average 83 stars, based on 5 article reviews
    Price from $9.99 to $1999.99
    cenp a mononucleosome - by Bioz Stars, 2020-02
    83/100 stars
      Buy from Supplier

    83
    EpiCypher recombinant human mononucleosomes
    Number of binding sites identified in treatment and control sample using different sets of parameters . (A - C) Box-plots show the ratios of predicted binding site counts in treatment and control achieved with different parameter choices. Lower values suggest higher specificity. (D) The number of predicted nucleosomes in the control sample is plotted versus the number of nucleosomes identified from the <t>mononucleosome</t> sample. Different colours correspond to different background rate cut-offs while different symbols indicate different cut-off levels for support region rates.
    Recombinant Human Mononucleosomes, supplied by EpiCypher, used in various techniques. Bioz Stars score: 83/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/recombinant human mononucleosomes/product/EpiCypher
    Average 83 stars, based on 5 article reviews
    Price from $9.99 to $1999.99
    recombinant human mononucleosomes - by Bioz Stars, 2020-02
    83/100 stars
      Buy from Supplier

    80
    EpiCypher human biotinylated mononucleosomes
    Number of binding sites identified in treatment and control sample using different sets of parameters . (A - C) Box-plots show the ratios of predicted binding site counts in treatment and control achieved with different parameter choices. Lower values suggest higher specificity. (D) The number of predicted nucleosomes in the control sample is plotted versus the number of nucleosomes identified from the <t>mononucleosome</t> sample. Different colours correspond to different background rate cut-offs while different symbols indicate different cut-off levels for support region rates.
    Human Biotinylated Mononucleosomes, supplied by EpiCypher, used in various techniques. Bioz Stars score: 80/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/human biotinylated mononucleosomes/product/EpiCypher
    Average 80 stars, based on 8 article reviews
    Price from $9.99 to $1999.99
    human biotinylated mononucleosomes - by Bioz Stars, 2020-02
    80/100 stars
      Buy from Supplier

    91
    EpiCypher recombinant mononucleosomes
    Number of binding sites identified in treatment and control sample using different sets of parameters . (A - C) Box-plots show the ratios of predicted binding site counts in treatment and control achieved with different parameter choices. Lower values suggest higher specificity. (D) The number of predicted nucleosomes in the control sample is plotted versus the number of nucleosomes identified from the <t>mononucleosome</t> sample. Different colours correspond to different background rate cut-offs while different symbols indicate different cut-off levels for support region rates.
    Recombinant Mononucleosomes, supplied by EpiCypher, used in various techniques. Bioz Stars score: 91/100, based on 18 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/recombinant mononucleosomes/product/EpiCypher
    Average 91 stars, based on 18 article reviews
    Price from $9.99 to $1999.99
    recombinant mononucleosomes - by Bioz Stars, 2020-02
    91/100 stars
      Buy from Supplier

    77
    Illumina Inc mononucleosomal size range
    Number of binding sites identified in treatment and control sample using different sets of parameters . (A - C) Box-plots show the ratios of predicted binding site counts in treatment and control achieved with different parameter choices. Lower values suggest higher specificity. (D) The number of predicted nucleosomes in the control sample is plotted versus the number of nucleosomes identified from the <t>mononucleosome</t> sample. Different colours correspond to different background rate cut-offs while different symbols indicate different cut-off levels for support region rates.
    Mononucleosomal Size Range, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 77/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/mononucleosomal size range/product/Illumina Inc
    Average 77 stars, based on 5 article reviews
    Price from $9.99 to $1999.99
    mononucleosomal size range - by Bioz Stars, 2020-02
    77/100 stars
      Buy from Supplier

    95
    Illumina Inc mononucleosomal dna
    Trinucleotide profiles predict the distribution of amino acids encoded by <t>mononucleosomal</t> <t>DNA.</t> The aggregated profile of trinucleotides corresponding to codons for the 20 amino acids (red) coincides with the actual profile of amino acid distribution in proteins (blue) in S. pombe and S. cerevisiae . The y -axis indicates the relative frequency of aggregated trinucleotides (red) normalized to the average genomic composition and the relative frequency of amino acids (blue) encoded by mononucleosomal DNA in ORFs. The x -axis represents the distance relative to the central position of mononucleosomal DNA. Results for S. octosporus and S. japonicus are shown in the electronic supplementary material, figure S7.
    Mononucleosomal Dna, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 95/100, based on 147 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/mononucleosomal dna/product/Illumina Inc
    Average 95 stars, based on 147 article reviews
    Price from $9.99 to $1999.99
    mononucleosomal dna - by Bioz Stars, 2020-02
    95/100 stars
      Buy from Supplier

    76
    Promega mononucleosome sized fragments
    Trinucleotide profiles predict the distribution of amino acids encoded by <t>mononucleosomal</t> <t>DNA.</t> The aggregated profile of trinucleotides corresponding to codons for the 20 amino acids (red) coincides with the actual profile of amino acid distribution in proteins (blue) in S. pombe and S. cerevisiae . The y -axis indicates the relative frequency of aggregated trinucleotides (red) normalized to the average genomic composition and the relative frequency of amino acids (blue) encoded by mononucleosomal DNA in ORFs. The x -axis represents the distance relative to the central position of mononucleosomal DNA. Results for S. octosporus and S. japonicus are shown in the electronic supplementary material, figure S7.
    Mononucleosome Sized Fragments, supplied by Promega, used in various techniques. Bioz Stars score: 76/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/mononucleosome sized fragments/product/Promega
    Average 76 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    mononucleosome sized fragments - by Bioz Stars, 2020-02
    76/100 stars
      Buy from Supplier

    83
    ATUM mononucleosomal dna
    DMC treatment inhibits the interaction of proteins with the <t>DNA.</t> ( A ) Nuclei were isolated from MCF7 cells and treated with MNase to obtain mononucleosome fragmented DNA (150 bp). <t>Mononucleosomal</t> DNA was extracted and labeled with [ 32 P]. DNA-binding activity of nuclear proteins of untreated, 10 μM MC or DMC treated for 4 hours was analyzed by EMSA. ( B ) The cell cycle profile was checked by Fluorescence activated cell sorting (FACS). MCF7 cells left untreated, or treated with 10 μM MC or DMC for 4 hours and fixed in 30% ethanol and cellular DNA were stained with propidium iodide. ( C ) Chromatin immunoprecipitation (ChIP) was carried out in untreated, 10 μM MC or DMC treated for 4 hours and UV (50J/m 2 ) irradiated MCF7 cells. ChIP was performed in 400 μg of cross-linked and sonicated cell lysates and antibody against ATR. Immunoprecipitated DNA was amplified by real-time quantitative PCR with primers for p53 intron 7 gene. Non-specific IgG was used to subtract the background. Values were normalized to IgG and inputs, followed by normalization to the untreated samples.
    Mononucleosomal Dna, supplied by ATUM, used in various techniques. Bioz Stars score: 83/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/mononucleosomal dna/product/ATUM
    Average 83 stars, based on 10 article reviews
    Price from $9.99 to $1999.99
    mononucleosomal dna - by Bioz Stars, 2020-02
    83/100 stars
      Buy from Supplier

    78
    EpiCypher recombinant xenopus mononucleosomes
    DMC treatment inhibits the interaction of proteins with the <t>DNA.</t> ( A ) Nuclei were isolated from MCF7 cells and treated with MNase to obtain mononucleosome fragmented DNA (150 bp). <t>Mononucleosomal</t> DNA was extracted and labeled with [ 32 P]. DNA-binding activity of nuclear proteins of untreated, 10 μM MC or DMC treated for 4 hours was analyzed by EMSA. ( B ) The cell cycle profile was checked by Fluorescence activated cell sorting (FACS). MCF7 cells left untreated, or treated with 10 μM MC or DMC for 4 hours and fixed in 30% ethanol and cellular DNA were stained with propidium iodide. ( C ) Chromatin immunoprecipitation (ChIP) was carried out in untreated, 10 μM MC or DMC treated for 4 hours and UV (50J/m 2 ) irradiated MCF7 cells. ChIP was performed in 400 μg of cross-linked and sonicated cell lysates and antibody against ATR. Immunoprecipitated DNA was amplified by real-time quantitative PCR with primers for p53 intron 7 gene. Non-specific IgG was used to subtract the background. Values were normalized to IgG and inputs, followed by normalization to the untreated samples.
    Recombinant Xenopus Mononucleosomes, supplied by EpiCypher, used in various techniques. Bioz Stars score: 78/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/recombinant xenopus mononucleosomes/product/EpiCypher
    Average 78 stars, based on 4 article reviews
    Price from $9.99 to $1999.99
    recombinant xenopus mononucleosomes - by Bioz Stars, 2020-02
    78/100 stars
      Buy from Supplier

    77
    Solexa mononucleosome associated dna
    DMC treatment inhibits the interaction of proteins with the <t>DNA.</t> ( A ) Nuclei were isolated from MCF7 cells and treated with MNase to obtain mononucleosome fragmented DNA (150 bp). <t>Mononucleosomal</t> DNA was extracted and labeled with [ 32 P]. DNA-binding activity of nuclear proteins of untreated, 10 μM MC or DMC treated for 4 hours was analyzed by EMSA. ( B ) The cell cycle profile was checked by Fluorescence activated cell sorting (FACS). MCF7 cells left untreated, or treated with 10 μM MC or DMC for 4 hours and fixed in 30% ethanol and cellular DNA were stained with propidium iodide. ( C ) Chromatin immunoprecipitation (ChIP) was carried out in untreated, 10 μM MC or DMC treated for 4 hours and UV (50J/m 2 ) irradiated MCF7 cells. ChIP was performed in 400 μg of cross-linked and sonicated cell lysates and antibody against ATR. Immunoprecipitated DNA was amplified by real-time quantitative PCR with primers for p53 intron 7 gene. Non-specific IgG was used to subtract the background. Values were normalized to IgG and inputs, followed by normalization to the untreated samples.
    Mononucleosome Associated Dna, supplied by Solexa, used in various techniques. Bioz Stars score: 77/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/mononucleosome associated dna/product/Solexa
    Average 77 stars, based on 5 article reviews
    Price from $9.99 to $1999.99
    mononucleosome associated dna - by Bioz Stars, 2020-02
    77/100 stars
      Buy from Supplier

    79
    Illumina Inc mononucleosome dna isolation
    DMC treatment inhibits the interaction of proteins with the <t>DNA.</t> ( A ) Nuclei were isolated from MCF7 cells and treated with MNase to obtain mononucleosome fragmented DNA (150 bp). <t>Mononucleosomal</t> DNA was extracted and labeled with [ 32 P]. DNA-binding activity of nuclear proteins of untreated, 10 μM MC or DMC treated for 4 hours was analyzed by EMSA. ( B ) The cell cycle profile was checked by Fluorescence activated cell sorting (FACS). MCF7 cells left untreated, or treated with 10 μM MC or DMC for 4 hours and fixed in 30% ethanol and cellular DNA were stained with propidium iodide. ( C ) Chromatin immunoprecipitation (ChIP) was carried out in untreated, 10 μM MC or DMC treated for 4 hours and UV (50J/m 2 ) irradiated MCF7 cells. ChIP was performed in 400 μg of cross-linked and sonicated cell lysates and antibody against ATR. Immunoprecipitated DNA was amplified by real-time quantitative PCR with primers for p53 intron 7 gene. Non-specific IgG was used to subtract the background. Values were normalized to IgG and inputs, followed by normalization to the untreated samples.
    Mononucleosome Dna Isolation, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 79/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/mononucleosome dna isolation/product/Illumina Inc
    Average 79 stars, based on 5 article reviews
    Price from $9.99 to $1999.99
    mononucleosome dna isolation - by Bioz Stars, 2020-02
    79/100 stars
      Buy from Supplier

    80
    Thermo Fisher dsdna mononucleosome assembly oligonucleotides
    DMC treatment inhibits the interaction of proteins with the <t>DNA.</t> ( A ) Nuclei were isolated from MCF7 cells and treated with MNase to obtain mononucleosome fragmented DNA (150 bp). <t>Mononucleosomal</t> DNA was extracted and labeled with [ 32 P]. DNA-binding activity of nuclear proteins of untreated, 10 μM MC or DMC treated for 4 hours was analyzed by EMSA. ( B ) The cell cycle profile was checked by Fluorescence activated cell sorting (FACS). MCF7 cells left untreated, or treated with 10 μM MC or DMC for 4 hours and fixed in 30% ethanol and cellular DNA were stained with propidium iodide. ( C ) Chromatin immunoprecipitation (ChIP) was carried out in untreated, 10 μM MC or DMC treated for 4 hours and UV (50J/m 2 ) irradiated MCF7 cells. ChIP was performed in 400 μg of cross-linked and sonicated cell lysates and antibody against ATR. Immunoprecipitated DNA was amplified by real-time quantitative PCR with primers for p53 intron 7 gene. Non-specific IgG was used to subtract the background. Values were normalized to IgG and inputs, followed by normalization to the untreated samples.
    Dsdna Mononucleosome Assembly Oligonucleotides, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 80/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dsdna mononucleosome assembly oligonucleotides/product/Thermo Fisher
    Average 80 stars, based on 8 article reviews
    Price from $9.99 to $1999.99
    dsdna mononucleosome assembly oligonucleotides - by Bioz Stars, 2020-02
    80/100 stars
      Buy from Supplier

    78
    Illumina Inc mononucleosomal illumina sequencing coverage plots
    DMC treatment inhibits the interaction of proteins with the <t>DNA.</t> ( A ) Nuclei were isolated from MCF7 cells and treated with MNase to obtain mononucleosome fragmented DNA (150 bp). <t>Mononucleosomal</t> DNA was extracted and labeled with [ 32 P]. DNA-binding activity of nuclear proteins of untreated, 10 μM MC or DMC treated for 4 hours was analyzed by EMSA. ( B ) The cell cycle profile was checked by Fluorescence activated cell sorting (FACS). MCF7 cells left untreated, or treated with 10 μM MC or DMC for 4 hours and fixed in 30% ethanol and cellular DNA were stained with propidium iodide. ( C ) Chromatin immunoprecipitation (ChIP) was carried out in untreated, 10 μM MC or DMC treated for 4 hours and UV (50J/m 2 ) irradiated MCF7 cells. ChIP was performed in 400 μg of cross-linked and sonicated cell lysates and antibody against ATR. Immunoprecipitated DNA was amplified by real-time quantitative PCR with primers for p53 intron 7 gene. Non-specific IgG was used to subtract the background. Values were normalized to IgG and inputs, followed by normalization to the untreated samples.
    Mononucleosomal Illumina Sequencing Coverage Plots, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 78/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/mononucleosomal illumina sequencing coverage plots/product/Illumina Inc
    Average 78 stars, based on 6 article reviews
    Price from $9.99 to $1999.99
    mononucleosomal illumina sequencing coverage plots - by Bioz Stars, 2020-02
    78/100 stars
      Buy from Supplier

    Image Search Results


    UHRF1 and UHRF2 diverge in their ability to ubiquitinate nucleosomal histones. ( A ) Chromatin association assays for FLAG-tagged UHRF2 (WT) or the indicated mutants from asynchronously growing HeLa cells. Mock treatment represents an empty vector control. ( B ) Comparative in vitro ubiquitination of H3 (1–32) K9me2 (left) and HeLa mononucleosomes (right) by UHRF1 and UHRF2. Moles of H3 are equivalent in these reactions.

    Journal: Nucleic Acids Research

    Article Title: Comparative biochemical analysis of UHRF proteins reveals molecular mechanisms that uncouple UHRF2 from DNA methylation maintenance

    doi: 10.1093/nar/gky151

    Figure Lengend Snippet: UHRF1 and UHRF2 diverge in their ability to ubiquitinate nucleosomal histones. ( A ) Chromatin association assays for FLAG-tagged UHRF2 (WT) or the indicated mutants from asynchronously growing HeLa cells. Mock treatment represents an empty vector control. ( B ) Comparative in vitro ubiquitination of H3 (1–32) K9me2 (left) and HeLa mononucleosomes (right) by UHRF1 and UHRF2. Moles of H3 are equivalent in these reactions.

    Article Snippet: For in vitro ubiquitination of HeLa mononucleosomes, reactions were run in ubiquitin assay buffer containing 1.5 μM E3, 50 nM E1 UBA1, 667 nM E2 UBCH5A, 5 μM TAMRA-ubiquitin, and 0.5 μM HeLa mononucleosomes (Epicypher).

    Techniques: Plasmid Preparation, In Vitro

    Characterizing lysine prioritization of UHRF1 ubiquitylation on mononucleosomes. ( A ) Ubiquitylation of Hela mononucleosomes after 2 hr in the presence of HeDNA or UnDNA. ( B ) Ratio and normalized ratio (HeDNA/UnDNA) for H3 ubiquitylated peptides from propionylated samples. Samples were normalized to the mean ratio of free ubiquitin peptides. Quantification was performed with Skyline and values for each peptide charge state were summed. ( C ) Ratio and normalized ratio (HeDNA/UnDNA) for H3 ubiquitylated peptides from propionylated and unreacted samples. A ubiquitylated peptide from the PHD (marked with an asterisk) wa s enriched in the HeDNA sample. ( D ) Location of UHRF1 auto-ubiquitylation sites lining the TTD-PHD. TTD, pink; PHD, blue; modified lysines, red. The C-terminal atom on the H3 peptide (S10) is shown as a sphere. ( E ) Auto-ubiquitylation of UHRF1 in the absence of H3 peptides with either HeDNA or UnDNA when run under conditions to resolve higher molecular weight species. DOI: http://dx.doi.org/10.7554/eLife.17101.015

    Journal: eLife

    Article Title: Hemi-methylated DNA regulates DNA methylation inheritance through allosteric activation of H3 ubiquitylation by UHRF1

    doi: 10.7554/eLife.17101

    Figure Lengend Snippet: Characterizing lysine prioritization of UHRF1 ubiquitylation on mononucleosomes. ( A ) Ubiquitylation of Hela mononucleosomes after 2 hr in the presence of HeDNA or UnDNA. ( B ) Ratio and normalized ratio (HeDNA/UnDNA) for H3 ubiquitylated peptides from propionylated samples. Samples were normalized to the mean ratio of free ubiquitin peptides. Quantification was performed with Skyline and values for each peptide charge state were summed. ( C ) Ratio and normalized ratio (HeDNA/UnDNA) for H3 ubiquitylated peptides from propionylated and unreacted samples. A ubiquitylated peptide from the PHD (marked with an asterisk) wa s enriched in the HeDNA sample. ( D ) Location of UHRF1 auto-ubiquitylation sites lining the TTD-PHD. TTD, pink; PHD, blue; modified lysines, red. The C-terminal atom on the H3 peptide (S10) is shown as a sphere. ( E ) Auto-ubiquitylation of UHRF1 in the absence of H3 peptides with either HeDNA or UnDNA when run under conditions to resolve higher molecular weight species. DOI: http://dx.doi.org/10.7554/eLife.17101.015

    Article Snippet: Recombinant histone proteins and mononucleosomes were obtained commercially from Epicypher (H2A, #15–0301; H2B, 15–0302; and H3.1, #15–0303; mononucleosomes, #16–0002; Research Triangle Park, NC).

    Techniques: Modification, Molecular Weight

    UHRF1 ubiquitin ligase assays. ( A ) Time course assay of UHRF1 auto-ubiquitylation in the presence of UnDNA or HeDNA in the absence of a histone peptide substrate (left). Rates of UHRF1 auto-ubiquitylation (right) were quantified from blots using ImageQuant TL (GE Lifesciences). Quantified data was best described by a linear fit over the measured time scale. ( B ) UHRF1 ubiquitylation of HeLa mononucleosomes in the presence or absence of HeDNA reveals that mononucleosome ubiquitylation is significantly enhanced in the presence of HeDNA. ( C ) Ubiquitylation of H3 1-32 K9me2 by MBP-tagged UHRF1 and the indicated mutants. Mutant UHRF1 proteins display significant defects in HeDNA stimulated ubiquitylation activity with the exception of the D469G. ( D ) FP binding assays quantifying the interaction of the MBP-UHRF1 D469G with FAM-labeled HeDNA, SyDNA, or UnDNA. Error is represented as ± s.e.m. for two independent experiments. While the literature suggests a HeDNA binding defect for the D469G mutation, these assays reveal this mutant binds DNA similarly to wild-type (for comparison see Figure 1B ). DOI: http://dx.doi.org/10.7554/eLife.17101.010

    Journal: eLife

    Article Title: Hemi-methylated DNA regulates DNA methylation inheritance through allosteric activation of H3 ubiquitylation by UHRF1

    doi: 10.7554/eLife.17101

    Figure Lengend Snippet: UHRF1 ubiquitin ligase assays. ( A ) Time course assay of UHRF1 auto-ubiquitylation in the presence of UnDNA or HeDNA in the absence of a histone peptide substrate (left). Rates of UHRF1 auto-ubiquitylation (right) were quantified from blots using ImageQuant TL (GE Lifesciences). Quantified data was best described by a linear fit over the measured time scale. ( B ) UHRF1 ubiquitylation of HeLa mononucleosomes in the presence or absence of HeDNA reveals that mononucleosome ubiquitylation is significantly enhanced in the presence of HeDNA. ( C ) Ubiquitylation of H3 1-32 K9me2 by MBP-tagged UHRF1 and the indicated mutants. Mutant UHRF1 proteins display significant defects in HeDNA stimulated ubiquitylation activity with the exception of the D469G. ( D ) FP binding assays quantifying the interaction of the MBP-UHRF1 D469G with FAM-labeled HeDNA, SyDNA, or UnDNA. Error is represented as ± s.e.m. for two independent experiments. While the literature suggests a HeDNA binding defect for the D469G mutation, these assays reveal this mutant binds DNA similarly to wild-type (for comparison see Figure 1B ). DOI: http://dx.doi.org/10.7554/eLife.17101.010

    Article Snippet: Recombinant histone proteins and mononucleosomes were obtained commercially from Epicypher (H2A, #15–0301; H2B, 15–0302; and H3.1, #15–0303; mononucleosomes, #16–0002; Research Triangle Park, NC).

    Techniques: Mutagenesis, Activity Assay, Binding Assay, Labeling

    Mononucleosome preparation from H3 D /H3 H cells. ( A ) Mononucleosomes were prepared from H3 D /H3 H cells, and purified by fast protein liquid chromatography. Molecular standards are labeled above the elution profile. ( B ) Fractions around the peak fractions (No. 14 to 31) were collected and denatured. The length of DNA was analyzed in a 2% agarose gel. Size markers are on the left. ( C ) Histone H3 in the fractions (labeled on top) was examined by western blotting using the anti-H3 N-terminal antibody. Fraction 26 was selected as mononucleosomes for further experiments.

    Journal: eLife

    Article Title: Independent manipulation of histone H3 modifications in individual nucleosomes reveals the contributions of sister histones to transcription

    doi: 10.7554/eLife.30178

    Figure Lengend Snippet: Mononucleosome preparation from H3 D /H3 H cells. ( A ) Mononucleosomes were prepared from H3 D /H3 H cells, and purified by fast protein liquid chromatography. Molecular standards are labeled above the elution profile. ( B ) Fractions around the peak fractions (No. 14 to 31) were collected and denatured. The length of DNA was analyzed in a 2% agarose gel. Size markers are on the left. ( C ) Histone H3 in the fractions (labeled on top) was examined by western blotting using the anti-H3 N-terminal antibody. Fraction 26 was selected as mononucleosomes for further experiments.

    Article Snippet: By the way, we compared our FPLC spectra for purification of mononucleosomes with the reference spectra of our chromatographic column provided by GE healthcare.

    Techniques: Purification, Fast Protein Liquid Chromatography, Labeling, Agarose Gel Electrophoresis, Western Blot

    Number of binding sites identified in treatment and control sample using different sets of parameters . (A - C) Box-plots show the ratios of predicted binding site counts in treatment and control achieved with different parameter choices. Lower values suggest higher specificity. (D) The number of predicted nucleosomes in the control sample is plotted versus the number of nucleosomes identified from the mononucleosome sample. Different colours correspond to different background rate cut-offs while different symbols indicate different cut-off levels for support region rates.

    Journal: BMC Bioinformatics

    Article Title: ChIPseqR: analysis of ChIP-seq experiments

    doi: 10.1186/1471-2105-12-39

    Figure Lengend Snippet: Number of binding sites identified in treatment and control sample using different sets of parameters . (A - C) Box-plots show the ratios of predicted binding site counts in treatment and control achieved with different parameter choices. Lower values suggest higher specificity. (D) The number of predicted nucleosomes in the control sample is plotted versus the number of nucleosomes identified from the mononucleosome sample. Different colours correspond to different background rate cut-offs while different symbols indicate different cut-off levels for support region rates.

    Article Snippet: The purified mononucleosome cores were then used to generate a library for Illumina GS sequencing (carried out by Geneworks, Adelaide, Australia) or used for qPCR quantification.

    Techniques: Binding Assay

    Trinucleotide profiles predict the distribution of amino acids encoded by mononucleosomal DNA. The aggregated profile of trinucleotides corresponding to codons for the 20 amino acids (red) coincides with the actual profile of amino acid distribution in proteins (blue) in S. pombe and S. cerevisiae . The y -axis indicates the relative frequency of aggregated trinucleotides (red) normalized to the average genomic composition and the relative frequency of amino acids (blue) encoded by mononucleosomal DNA in ORFs. The x -axis represents the distance relative to the central position of mononucleosomal DNA. Results for S. octosporus and S. japonicus are shown in the electronic supplementary material, figure S7.

    Journal: Open Biology

    Article Title: A species-specific nucleosomal signature defines a periodic distribution of amino acids in proteins

    doi: 10.1098/rsob.140218

    Figure Lengend Snippet: Trinucleotide profiles predict the distribution of amino acids encoded by mononucleosomal DNA. The aggregated profile of trinucleotides corresponding to codons for the 20 amino acids (red) coincides with the actual profile of amino acid distribution in proteins (blue) in S. pombe and S. cerevisiae . The y -axis indicates the relative frequency of aggregated trinucleotides (red) normalized to the average genomic composition and the relative frequency of amino acids (blue) encoded by mononucleosomal DNA in ORFs. The x -axis represents the distance relative to the central position of mononucleosomal DNA. Results for S. octosporus and S. japonicus are shown in the electronic supplementary material, figure S7.

    Article Snippet: Sequencing and alignment of sequence reads Mononucleosomal DNA was sequenced with an Illumina Genome Analyzer IIx using the single-read sequencing protocol.

    Techniques:

    Periodic distribution of amino acids along ORFs. The same average distribution of amino acids encoded by mononucleosomal DNA from different nucleosomes generates a periodic profile along ORFs. Small differences between nucleosomes at different positions are due to the fact that the number of sequences analysed in each of the six cases is lower than in figure 3 . The y -axis indicates the relative frequency of amino acids. The x -axis indicates the number of codons along the six groups of mononucleosomal DNA. The bottom diagram represents the position of the two nucleosomes immediately downstream from the ATG codon (A1 and A2) and another two mapping to the centre of ORFs (C1 and C2) or immediately upstream from the STOP codon (S1 and S2). Arrows represent their position along a generic ORF.

    Journal: Open Biology

    Article Title: A species-specific nucleosomal signature defines a periodic distribution of amino acids in proteins

    doi: 10.1098/rsob.140218

    Figure Lengend Snippet: Periodic distribution of amino acids along ORFs. The same average distribution of amino acids encoded by mononucleosomal DNA from different nucleosomes generates a periodic profile along ORFs. Small differences between nucleosomes at different positions are due to the fact that the number of sequences analysed in each of the six cases is lower than in figure 3 . The y -axis indicates the relative frequency of amino acids. The x -axis indicates the number of codons along the six groups of mononucleosomal DNA. The bottom diagram represents the position of the two nucleosomes immediately downstream from the ATG codon (A1 and A2) and another two mapping to the centre of ORFs (C1 and C2) or immediately upstream from the STOP codon (S1 and S2). Arrows represent their position along a generic ORF.

    Article Snippet: Sequencing and alignment of sequence reads Mononucleosomal DNA was sequenced with an Illumina Genome Analyzer IIx using the single-read sequencing protocol.

    Techniques:

    Patterns of nucleotide distribution across mononucleosomal DNA. ( a ) Base composition profiles of the four nucleotides across 38 154, 46 120, 27 024 and 34 526 mononucleosomal DNA sequences from the whole genome of S. pombe, S. octosporus, S. japonicus and S. cerevisiae , respectively, aligned to their central position. ( b ) Profiles of the same number of DNA fragments of the same length as in ( a ) selected at random from the genome of each species. ( c ) A + T content of the mononucleosomal DNA sequences shown in ( a ). The x -axis indicates positions relative to the centre of mononucleosomal DNA.

    Journal: Open Biology

    Article Title: A species-specific nucleosomal signature defines a periodic distribution of amino acids in proteins

    doi: 10.1098/rsob.140218

    Figure Lengend Snippet: Patterns of nucleotide distribution across mononucleosomal DNA. ( a ) Base composition profiles of the four nucleotides across 38 154, 46 120, 27 024 and 34 526 mononucleosomal DNA sequences from the whole genome of S. pombe, S. octosporus, S. japonicus and S. cerevisiae , respectively, aligned to their central position. ( b ) Profiles of the same number of DNA fragments of the same length as in ( a ) selected at random from the genome of each species. ( c ) A + T content of the mononucleosomal DNA sequences shown in ( a ). The x -axis indicates positions relative to the centre of mononucleosomal DNA.

    Article Snippet: Sequencing and alignment of sequence reads Mononucleosomal DNA was sequenced with an Illumina Genome Analyzer IIx using the single-read sequencing protocol.

    Techniques:

    Trinucleotide profiles of mononucleosomal DNA. The frequencies of trinucleotides across mononucleosomal DNA (blue) corresponding to the codons for alanine and lysine in S. pombe, S. octosporus, S. japonicus and S. cerevisiae were grouped in aggregated profiles (red). The y -axis indicates the relative frequency of each trinucleotide (blue) or their aggregated value (red) normalized to the genomic average. The x -axis represents the distance relative to the central position of mononucleosomal DNA. The complete set of profiles for the 61 coding codons corresponding to the 20 amino acids in the four species is shown in the electronic supplementary material, figure S6.

    Journal: Open Biology

    Article Title: A species-specific nucleosomal signature defines a periodic distribution of amino acids in proteins

    doi: 10.1098/rsob.140218

    Figure Lengend Snippet: Trinucleotide profiles of mononucleosomal DNA. The frequencies of trinucleotides across mononucleosomal DNA (blue) corresponding to the codons for alanine and lysine in S. pombe, S. octosporus, S. japonicus and S. cerevisiae were grouped in aggregated profiles (red). The y -axis indicates the relative frequency of each trinucleotide (blue) or their aggregated value (red) normalized to the genomic average. The x -axis represents the distance relative to the central position of mononucleosomal DNA. The complete set of profiles for the 61 coding codons corresponding to the 20 amino acids in the four species is shown in the electronic supplementary material, figure S6.

    Article Snippet: Sequencing and alignment of sequence reads Mononucleosomal DNA was sequenced with an Illumina Genome Analyzer IIx using the single-read sequencing protocol.

    Techniques:

    DMC treatment inhibits the interaction of proteins with the DNA. ( A ) Nuclei were isolated from MCF7 cells and treated with MNase to obtain mononucleosome fragmented DNA (150 bp). Mononucleosomal DNA was extracted and labeled with [ 32 P]. DNA-binding activity of nuclear proteins of untreated, 10 μM MC or DMC treated for 4 hours was analyzed by EMSA. ( B ) The cell cycle profile was checked by Fluorescence activated cell sorting (FACS). MCF7 cells left untreated, or treated with 10 μM MC or DMC for 4 hours and fixed in 30% ethanol and cellular DNA were stained with propidium iodide. ( C ) Chromatin immunoprecipitation (ChIP) was carried out in untreated, 10 μM MC or DMC treated for 4 hours and UV (50J/m 2 ) irradiated MCF7 cells. ChIP was performed in 400 μg of cross-linked and sonicated cell lysates and antibody against ATR. Immunoprecipitated DNA was amplified by real-time quantitative PCR with primers for p53 intron 7 gene. Non-specific IgG was used to subtract the background. Values were normalized to IgG and inputs, followed by normalization to the untreated samples.

    Journal: Cell Cycle

    Article Title: Decarbamoyl mitomycin C (DMC) activates p53-independent ataxia telangiectasia and rad3 related protein (ATR) chromatin eviction

    doi: 10.1080/15384101.2014.997517

    Figure Lengend Snippet: DMC treatment inhibits the interaction of proteins with the DNA. ( A ) Nuclei were isolated from MCF7 cells and treated with MNase to obtain mononucleosome fragmented DNA (150 bp). Mononucleosomal DNA was extracted and labeled with [ 32 P]. DNA-binding activity of nuclear proteins of untreated, 10 μM MC or DMC treated for 4 hours was analyzed by EMSA. ( B ) The cell cycle profile was checked by Fluorescence activated cell sorting (FACS). MCF7 cells left untreated, or treated with 10 μM MC or DMC for 4 hours and fixed in 30% ethanol and cellular DNA were stained with propidium iodide. ( C ) Chromatin immunoprecipitation (ChIP) was carried out in untreated, 10 μM MC or DMC treated for 4 hours and UV (50J/m 2 ) irradiated MCF7 cells. ChIP was performed in 400 μg of cross-linked and sonicated cell lysates and antibody against ATR. Immunoprecipitated DNA was amplified by real-time quantitative PCR with primers for p53 intron 7 gene. Non-specific IgG was used to subtract the background. Values were normalized to IgG and inputs, followed by normalization to the untreated samples.

    Article Snippet: Reaction mixtures for EMSA experiments (30 μl) were composed of 0.1 pmol of mononucleosomal DNA, 20 mM HEPES (pH 7.8), 100 mM KCl, 1 mM EDTA, 1 mM DTT, 1 μg of sonicated salmon sperm DNA, and 10% glycerol.

    Techniques: Isolation, Labeling, Binding Assay, Activity Assay, Fluorescence, FACS, Staining, Chromatin Immunoprecipitation, Irradiation, Sonication, Immunoprecipitation, Amplification, Real-time Polymerase Chain Reaction