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  • 99
    Worthington Biochemical micrococcal nuclease mnase
    Micrococcal Nuclease Mnase, supplied by Worthington Biochemical, used in various techniques. Bioz Stars score: 99/100, based on 98 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/micrococcal nuclease mnase/product/Worthington Biochemical
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    99
    New England Biolabs micrococcal nuclease
    Micrococcal Nuclease, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 2709 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/micrococcal nuclease/product/New England Biolabs
    Average 99 stars, based on 2709 article reviews
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    92
    Thermo Fisher mnase
    Digestion of different regions of the rDNA units with <t>MNase.</t> (A) Isolated 1- to 16-h embryonic nuclei were digested with MNase (0.5 U/μl) at <t>24°C</t> for 0, 1, or 4 min (lanes 2 to 4 of each panel). Purified (protein-free) genomic DNA was
    Mnase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 92/100, based on 519 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/mnase/product/Thermo Fisher
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    99
    Millipore mnase
    shRNA-mediated inactivation of ATRX does not alter subtelomeric chromatin accessibility to <t>MNase.</t> (A) Chromatin isolated from 8-MG-BA glioma cells in which ATRX had been inactivated (shATRX) or not (shscrambled [shSCR]) was digested with MNase for the indicated times. (Left gel) Ethidium bromide (EtBr) staining of bulk chromatin. (Right gel) Southern blot with subtelomeric probe. (Far right) Quantification of the data. The signals obtained for mononucleosomes were normalized to the total signals measured for each time point (EtBr or Southern blot). (B) Chromatin samples from shATRX or shSCR 8-MG-BA cells were digested for 5 min with the indicated amounts of MNase (milliunits per microgram of DNA). (Far right) Quantification of the data.
    Mnase, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 1141 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    mnase - by Bioz Stars, 2020-09
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    92
    Cell Signaling Technology Inc mnase
    shRNA-mediated inactivation of ATRX does not alter subtelomeric chromatin accessibility to <t>MNase.</t> (A) Chromatin isolated from 8-MG-BA glioma cells in which ATRX had been inactivated (shATRX) or not (shscrambled [shSCR]) was digested with MNase for the indicated times. (Left gel) Ethidium bromide (EtBr) staining of bulk chromatin. (Right gel) Southern blot with subtelomeric probe. (Far right) Quantification of the data. The signals obtained for mononucleosomes were normalized to the total signals measured for each time point (EtBr or Southern blot). (B) Chromatin samples from shATRX or shSCR 8-MG-BA cells were digested for 5 min with the indicated amounts of MNase (milliunits per microgram of DNA). (Far right) Quantification of the data.
    Mnase, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 92/100, based on 55 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/mnase/product/Cell Signaling Technology Inc
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    98
    Thermo Fisher micrococcal nuclease mnase
    VP2 binds to chromatin and interacts with MCM3 but this does not require dual phosphatase activity . ( A ) The soluble (S) and chromatin (C) fractions were prepared by using CSK buffer containing 0.5% Triton X-100 in CHO cells of transfected with VP2-GFP plasmid. The fractions were treated with 0 U (-) and 150 U (+) of <t>MNase</t> or the indicated concentrations of <t>NaCl.</t> Nuclear extracts (N) containing VP2-GFP were as positive control and all fractions were subjected to immunoblotting against with lamin B receptor, MCM3, and VP2 antibodies. ( B ) At 48 h post-transfection, the GFP (as Control) and Flag-VP2-GFP (as wild-type; WT) were found in the CHO cells. Next the lysates were immunoprecipitated using Flag M2 beads and immunoblotted against VP2 and MCM3 antibodies. ( C ) The WT and mutants (C95S, C97S, and C95S/C97S) of the Flag-VP2-GFP in CHO cells were also examined at 48 h post-transfection. The cell lysates were immunoprecipitated using Flag M2 beads and immunoblotted against with VP2 and MCM3 antibodies. The arrow head was indicated a none-specific band. The nuclear extracts containing VP2-GFP were designated as N
    Micrococcal Nuclease Mnase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 98/100, based on 40 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/micrococcal nuclease mnase/product/Thermo Fisher
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    90
    Illumina Inc micrococcal nuclease mnase
    Genome-wide nucleosome positioning in Dictyostelium . ( A ) Normalized read midpoint frequency distributions of <t>MNase-protected</t> fragments (nucleosome dyads) of all 12,750 genes in growth-stage WT cells were aligned relative to their ATG codons. Peaks (arrows) correspond to dyad midpoints for globally phased nucleosomes in the 5′ region of intragenic <t>DNA,</t> and distances between mapped read peaks correspond to ∼170 bp NRL. The protein coding DNA sequence (cds) region is shaded. ( B ) Normalized read midpoint frequency distributions of all genes in growth-stage WT cells were aligned relative to their translational termination sites (stop codons). Peaks (arrows) in the mean normalized frequency distribution correspond to globally phased nucleosomes in the 3′ region of intragenic DNA. The protein cds region is shaded. ( C ) Normalized dyad read midpoint frequency distributions for WT chromatin (CHR; dotted line) (see A ) were adjusted for sequence mappability by dividing with equivalent control data from MNase-digested naked (protein free) WT DNA (DNA; red line) and replotted as the ratio (CHR/DNA; thick black line) within 1.2 kb of flanking chromatin relative to ATG sites of all 12,750 genes. An ∼170-bp nucleosome-depleted (“free”) region (NDR) is centered near the AT-rich regions of Dictyostelium TSS. Positioned nucleosomes upstream (+) and downstream (−) to the NDR are indicated by arrows. The protein cds region is shaded.
    Micrococcal Nuclease Mnase, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 29 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/micrococcal nuclease mnase/product/Illumina Inc
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    88
    Illumina Inc mnase digested chromatin
    Fun30 is required for normal CEN -flanking nucleosome positioning and/or CEN core particle structure. A) Genome browser trace of Fun30 ChIP enrichment and nucleosome dyad frequency centred on and surrounding yeast CEN1 . The upper trace shows Log 2 Fun30 ChIP-seq enrichment values binned at 10 bp intervals and smoothed with a 3 bin moving average. Wildtype (WT) and Δfun30 chromatin was digested with <t>MNase</t> and nuclease-protected DNA species sequenced using paired-end mode <t>Illumina</t> technology. Nucleosome sequencing data (nuc) traces were plotted as mirror images in the lower panel. The graph shows a map of the centre point positions of paired sequence reads with end-to-end distances of 150 bp+/−20% wild-type and Δfun30 mutant chromatin samples surrounding CEN1 . The frequency distributions, which effectively map chromatin particle dyads, were binned at 10 bp intervals, and smoothed by applying a 3 bin moving average. Peaks in the dyad distributions correspond to translationally-positioned nucleosomes in the original genome. The CEN core particle is also mapped using this method and can be visualised as a small peak centred on the CEN region marked with a grey box. Pink bars show the positions of ORFs (B–D) Genome browser plots of Fun30 ChIP-seq and nucleosome sequence distributions as described above for CEN10, 11 and 12 respectively. Fun30-dependent changes in the height of a nucleosome dyad or CEN core particle peak are marked with a red asterix. Fun30-dependent changes in the position of a CEN -flanking nucleosome dyad peak are marked with red arrows. Genome browser plots for all yeast CENs are shown in Figure S6 .
    Mnase Digested Chromatin, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 88/100, based on 30 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/mnase digested chromatin/product/Illumina Inc
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    mnase digested chromatin - by Bioz Stars, 2020-09
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    99
    Millipore mnase digestion buffer
    Fun30 is required for normal CEN -flanking nucleosome positioning and/or CEN core particle structure. A) Genome browser trace of Fun30 ChIP enrichment and nucleosome dyad frequency centred on and surrounding yeast CEN1 . The upper trace shows Log 2 Fun30 ChIP-seq enrichment values binned at 10 bp intervals and smoothed with a 3 bin moving average. Wildtype (WT) and Δfun30 chromatin was digested with <t>MNase</t> and nuclease-protected DNA species sequenced using paired-end mode <t>Illumina</t> technology. Nucleosome sequencing data (nuc) traces were plotted as mirror images in the lower panel. The graph shows a map of the centre point positions of paired sequence reads with end-to-end distances of 150 bp+/−20% wild-type and Δfun30 mutant chromatin samples surrounding CEN1 . The frequency distributions, which effectively map chromatin particle dyads, were binned at 10 bp intervals, and smoothed by applying a 3 bin moving average. Peaks in the dyad distributions correspond to translationally-positioned nucleosomes in the original genome. The CEN core particle is also mapped using this method and can be visualised as a small peak centred on the CEN region marked with a grey box. Pink bars show the positions of ORFs (B–D) Genome browser plots of Fun30 ChIP-seq and nucleosome sequence distributions as described above for CEN10, 11 and 12 respectively. Fun30-dependent changes in the height of a nucleosome dyad or CEN core particle peak are marked with a red asterix. Fun30-dependent changes in the position of a CEN -flanking nucleosome dyad peak are marked with red arrows. Genome browser plots for all yeast CENs are shown in Figure S6 .
    Mnase Digestion Buffer, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 100 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    97
    TaKaRa micrococcal nuclease mnase
    Chromatin structure around ade6-3049 is more open than around ade6-3057 , and HRA is involved in the chromatin regulation. (A) <t>MNase</t> sensitivity of chromatin around ade6-3049/3057 . Indicated cells of the pat1-114 background were induced to enter meiosis by temperature-shift method, and harvested 3 hr after the induction. MNase-digested <t>DNA</t> was prepared by MNase (0, 20, or 30 units) treatment of chromatin fraction and subsequent purification. DNA was further cut with Sac I, fractionated on 1.2% agaraose gel, and analyzed by Southern blotting using the probe indicated by the open box. The vertical arrow and the open arrowhead show the ade6 ORF and the 3049/3057 site, respectively. The numbers on the left and the right side of the panel indicate the positions of λ/ Eco T14 I fragments used for electrophoresis marker and the positions from the first A of the ade6 ORF, respectively. The dotted lines indicate a region in which MNase-sensitive sites are clustered around ade6-3049 . Presented is an example from two independent experiments, whose results were similar to each other. (B) HRA deletion reduced acetylation level of H3K9 around ade6-3049 . Indicated cells of the pat1-114 ). DNA isolated from immunoprecipitates and whole-cell extracts was analyzed by real-time qPCR, where fragments corresponding to ade6-3049/3057 and the prp3 + promoter were amplified. Relative enrichment at ade6-3049/3057 over prp3 is shown. Bar graphs are created based on mean values of two independent experiments (shown by ○).
    Micrococcal Nuclease Mnase, supplied by TaKaRa, used in various techniques. Bioz Stars score: 97/100, based on 25 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Illumina Inc mnase seq
    Phased nucleosome arrays flanked TSSs of rice genes. (A) Nucleosome positioning profile associated with active genes. Phased nucleosome arrays are detectable after the TSSs. (B) Nucleosome positioning profile associated with non-expressed genes. Phased nucleosome arrays are detected on either side of the TSSs. (C) Distribution of DHS length for five different DHS categories. Note: the length of DHSs associated with proximal promoters (black line) are more variable than the lengths of other DHSs. (D) Heatmap of nucleosome positioning associated with active genes. Left panel: All expressed genes were sorted by the length of DHSs located in proximal promoters. The 5′ ends of the <t>MNase-seq</t> reads were mapped within 1 kb upstream and 1 kb downstream of the TSS of each gene to show the boundaries of <t>nucleosomes</t> core and linker. The red line on the left heatmap indicates the boundaries of DHSs. With the same order of the genes as in the left panel, the 5′ ends of DNase-seq reads (middle panel) and the fragments per kilobase of exon per million fragments mapped (FPKM) value log10 transformation (right panel) were mapped to show the DNase I sensitivity and the expression level of each gene, respectively.
    Mnase Seq, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 88/100, based on 29 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/mnase seq/product/Illumina Inc
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    88
    BioShop micrococcal nuclease s7
    Phased nucleosome arrays flanked TSSs of rice genes. (A) Nucleosome positioning profile associated with active genes. Phased nucleosome arrays are detectable after the TSSs. (B) Nucleosome positioning profile associated with non-expressed genes. Phased nucleosome arrays are detected on either side of the TSSs. (C) Distribution of DHS length for five different DHS categories. Note: the length of DHSs associated with proximal promoters (black line) are more variable than the lengths of other DHSs. (D) Heatmap of nucleosome positioning associated with active genes. Left panel: All expressed genes were sorted by the length of DHSs located in proximal promoters. The 5′ ends of the <t>MNase-seq</t> reads were mapped within 1 kb upstream and 1 kb downstream of the TSS of each gene to show the boundaries of <t>nucleosomes</t> core and linker. The red line on the left heatmap indicates the boundaries of DHSs. With the same order of the genes as in the left panel, the 5′ ends of DNase-seq reads (middle panel) and the fragments per kilobase of exon per million fragments mapped (FPKM) value log10 transformation (right panel) were mapped to show the DNase I sensitivity and the expression level of each gene, respectively.
    Micrococcal Nuclease S7, supplied by BioShop, used in various techniques. Bioz Stars score: 88/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Cell Signaling Technology Inc micrococcal nuclease mnase
    Phased nucleosome arrays flanked TSSs of rice genes. (A) Nucleosome positioning profile associated with active genes. Phased nucleosome arrays are detectable after the TSSs. (B) Nucleosome positioning profile associated with non-expressed genes. Phased nucleosome arrays are detected on either side of the TSSs. (C) Distribution of DHS length for five different DHS categories. Note: the length of DHSs associated with proximal promoters (black line) are more variable than the lengths of other DHSs. (D) Heatmap of nucleosome positioning associated with active genes. Left panel: All expressed genes were sorted by the length of DHSs located in proximal promoters. The 5′ ends of the <t>MNase-seq</t> reads were mapped within 1 kb upstream and 1 kb downstream of the TSS of each gene to show the boundaries of <t>nucleosomes</t> core and linker. The red line on the left heatmap indicates the boundaries of DHSs. With the same order of the genes as in the left panel, the 5′ ends of DNase-seq reads (middle panel) and the fragments per kilobase of exon per million fragments mapped (FPKM) value log10 transformation (right panel) were mapped to show the DNase I sensitivity and the expression level of each gene, respectively.
    Micrococcal Nuclease Mnase, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 99/100, based on 26 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/micrococcal nuclease mnase/product/Cell Signaling Technology Inc
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    99
    Millipore mnase buffer
    Phased nucleosome arrays flanked TSSs of rice genes. (A) Nucleosome positioning profile associated with active genes. Phased nucleosome arrays are detectable after the TSSs. (B) Nucleosome positioning profile associated with non-expressed genes. Phased nucleosome arrays are detected on either side of the TSSs. (C) Distribution of DHS length for five different DHS categories. Note: the length of DHSs associated with proximal promoters (black line) are more variable than the lengths of other DHSs. (D) Heatmap of nucleosome positioning associated with active genes. Left panel: All expressed genes were sorted by the length of DHSs located in proximal promoters. The 5′ ends of the <t>MNase-seq</t> reads were mapped within 1 kb upstream and 1 kb downstream of the TSS of each gene to show the boundaries of <t>nucleosomes</t> core and linker. The red line on the left heatmap indicates the boundaries of DHSs. With the same order of the genes as in the left panel, the 5′ ends of DNase-seq reads (middle panel) and the fragments per kilobase of exon per million fragments mapped (FPKM) value log10 transformation (right panel) were mapped to show the DNase I sensitivity and the expression level of each gene, respectively.
    Mnase Buffer, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 85 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Digestion of different regions of the rDNA units with MNase. (A) Isolated 1- to 16-h embryonic nuclei were digested with MNase (0.5 U/μl) at 24°C for 0, 1, or 4 min (lanes 2 to 4 of each panel). Purified (protein-free) genomic DNA was

    Journal: Molecular and Cellular Biology

    Article Title: Chromatin Structure and Transcription of the R1- and R2-Inserted rRNA Genes of Drosophila melanogaster ▿

    doi: 10.1128/MCB.01409-06

    Figure Lengend Snippet: Digestion of different regions of the rDNA units with MNase. (A) Isolated 1- to 16-h embryonic nuclei were digested with MNase (0.5 U/μl) at 24°C for 0, 1, or 4 min (lanes 2 to 4 of each panel). Purified (protein-free) genomic DNA was

    Article Snippet: For micrococcal nuclease (MNase) digestion, the nucleus solutions were made 3 mM CaCl2 and 0.5 units/μl MNase (Fermentas) and incubated at 24°C for the specified time.

    Techniques: Isolation, Purification

    shRNA-mediated inactivation of ATRX does not alter subtelomeric chromatin accessibility to MNase. (A) Chromatin isolated from 8-MG-BA glioma cells in which ATRX had been inactivated (shATRX) or not (shscrambled [shSCR]) was digested with MNase for the indicated times. (Left gel) Ethidium bromide (EtBr) staining of bulk chromatin. (Right gel) Southern blot with subtelomeric probe. (Far right) Quantification of the data. The signals obtained for mononucleosomes were normalized to the total signals measured for each time point (EtBr or Southern blot). (B) Chromatin samples from shATRX or shSCR 8-MG-BA cells were digested for 5 min with the indicated amounts of MNase (milliunits per microgram of DNA). (Far right) Quantification of the data.

    Journal: Molecular and Cellular Biology

    Article Title: Genetic Inactivation of ATRX Leads to a Decrease in the Amount of Telomeric Cohesin and Level of Telomere Transcription in Human Glioma Cells

    doi: 10.1128/MCB.01317-14

    Figure Lengend Snippet: shRNA-mediated inactivation of ATRX does not alter subtelomeric chromatin accessibility to MNase. (A) Chromatin isolated from 8-MG-BA glioma cells in which ATRX had been inactivated (shATRX) or not (shscrambled [shSCR]) was digested with MNase for the indicated times. (Left gel) Ethidium bromide (EtBr) staining of bulk chromatin. (Right gel) Southern blot with subtelomeric probe. (Far right) Quantification of the data. The signals obtained for mononucleosomes were normalized to the total signals measured for each time point (EtBr or Southern blot). (B) Chromatin samples from shATRX or shSCR 8-MG-BA cells were digested for 5 min with the indicated amounts of MNase (milliunits per microgram of DNA). (Far right) Quantification of the data.

    Article Snippet: Nuclei isolated from 107 cells were digested with 8 mU of micrococcal nuclease (MNase) (Sigma)/μg DNA at 37°C for the indicated times, as described previously ( ).

    Techniques: shRNA, Isolation, Staining, Southern Blot

    VP2 binds to chromatin and interacts with MCM3 but this does not require dual phosphatase activity . ( A ) The soluble (S) and chromatin (C) fractions were prepared by using CSK buffer containing 0.5% Triton X-100 in CHO cells of transfected with VP2-GFP plasmid. The fractions were treated with 0 U (-) and 150 U (+) of MNase or the indicated concentrations of NaCl. Nuclear extracts (N) containing VP2-GFP were as positive control and all fractions were subjected to immunoblotting against with lamin B receptor, MCM3, and VP2 antibodies. ( B ) At 48 h post-transfection, the GFP (as Control) and Flag-VP2-GFP (as wild-type; WT) were found in the CHO cells. Next the lysates were immunoprecipitated using Flag M2 beads and immunoblotted against VP2 and MCM3 antibodies. ( C ) The WT and mutants (C95S, C97S, and C95S/C97S) of the Flag-VP2-GFP in CHO cells were also examined at 48 h post-transfection. The cell lysates were immunoprecipitated using Flag M2 beads and immunoblotted against with VP2 and MCM3 antibodies. The arrow head was indicated a none-specific band. The nuclear extracts containing VP2-GFP were designated as N

    Journal: BMC Veterinary Research

    Article Title: Identification of the NLS and NES motifs of VP2 from chicken anemia virus and the interaction of VP2 with mini-chromosome maintenance protein 3

    doi: 10.1186/1746-6148-8-15

    Figure Lengend Snippet: VP2 binds to chromatin and interacts with MCM3 but this does not require dual phosphatase activity . ( A ) The soluble (S) and chromatin (C) fractions were prepared by using CSK buffer containing 0.5% Triton X-100 in CHO cells of transfected with VP2-GFP plasmid. The fractions were treated with 0 U (-) and 150 U (+) of MNase or the indicated concentrations of NaCl. Nuclear extracts (N) containing VP2-GFP were as positive control and all fractions were subjected to immunoblotting against with lamin B receptor, MCM3, and VP2 antibodies. ( B ) At 48 h post-transfection, the GFP (as Control) and Flag-VP2-GFP (as wild-type; WT) were found in the CHO cells. Next the lysates were immunoprecipitated using Flag M2 beads and immunoblotted against VP2 and MCM3 antibodies. ( C ) The WT and mutants (C95S, C97S, and C95S/C97S) of the Flag-VP2-GFP in CHO cells were also examined at 48 h post-transfection. The cell lysates were immunoprecipitated using Flag M2 beads and immunoblotted against with VP2 and MCM3 antibodies. The arrow head was indicated a none-specific band. The nuclear extracts containing VP2-GFP were designated as N

    Article Snippet: For micrococcal nuclease (MNase) (Fermentas, Canada) or NaCl treatment, the chromatin was resuspended in 100 μl of CSK buffer supplemented with 0.1 M, 0.3 M of NaCl or 0 U (-) and 150 U (+) MNase with 2 mM CaCl2 and incubated for 30 min at 37°C.

    Techniques: Activity Assay, Transfection, Plasmid Preparation, Positive Control, Immunoprecipitation

    Genome-wide nucleosome positioning in Dictyostelium . ( A ) Normalized read midpoint frequency distributions of MNase-protected fragments (nucleosome dyads) of all 12,750 genes in growth-stage WT cells were aligned relative to their ATG codons. Peaks (arrows) correspond to dyad midpoints for globally phased nucleosomes in the 5′ region of intragenic DNA, and distances between mapped read peaks correspond to ∼170 bp NRL. The protein coding DNA sequence (cds) region is shaded. ( B ) Normalized read midpoint frequency distributions of all genes in growth-stage WT cells were aligned relative to their translational termination sites (stop codons). Peaks (arrows) in the mean normalized frequency distribution correspond to globally phased nucleosomes in the 3′ region of intragenic DNA. The protein cds region is shaded. ( C ) Normalized dyad read midpoint frequency distributions for WT chromatin (CHR; dotted line) (see A ) were adjusted for sequence mappability by dividing with equivalent control data from MNase-digested naked (protein free) WT DNA (DNA; red line) and replotted as the ratio (CHR/DNA; thick black line) within 1.2 kb of flanking chromatin relative to ATG sites of all 12,750 genes. An ∼170-bp nucleosome-depleted (“free”) region (NDR) is centered near the AT-rich regions of Dictyostelium TSS. Positioned nucleosomes upstream (+) and downstream (−) to the NDR are indicated by arrows. The protein cds region is shaded.

    Journal: Genome Research

    Article Title: Regulation of nucleosome positioning by a CHD Type III chromatin remodeler and its relationship to developmental gene expression in Dictyostelium

    doi: 10.1101/gr.216309.116

    Figure Lengend Snippet: Genome-wide nucleosome positioning in Dictyostelium . ( A ) Normalized read midpoint frequency distributions of MNase-protected fragments (nucleosome dyads) of all 12,750 genes in growth-stage WT cells were aligned relative to their ATG codons. Peaks (arrows) correspond to dyad midpoints for globally phased nucleosomes in the 5′ region of intragenic DNA, and distances between mapped read peaks correspond to ∼170 bp NRL. The protein coding DNA sequence (cds) region is shaded. ( B ) Normalized read midpoint frequency distributions of all genes in growth-stage WT cells were aligned relative to their translational termination sites (stop codons). Peaks (arrows) in the mean normalized frequency distribution correspond to globally phased nucleosomes in the 3′ region of intragenic DNA. The protein cds region is shaded. ( C ) Normalized dyad read midpoint frequency distributions for WT chromatin (CHR; dotted line) (see A ) were adjusted for sequence mappability by dividing with equivalent control data from MNase-digested naked (protein free) WT DNA (DNA; red line) and replotted as the ratio (CHR/DNA; thick black line) within 1.2 kb of flanking chromatin relative to ATG sites of all 12,750 genes. An ∼170-bp nucleosome-depleted (“free”) region (NDR) is centered near the AT-rich regions of Dictyostelium TSS. Positioned nucleosomes upstream (+) and downstream (−) to the NDR are indicated by arrows. The protein cds region is shaded.

    Article Snippet: Chromatin was digested with micrococcal nuclease (MNase) to create nuclease-resistant DNA ladders with a fragment spectrum of < 1 kb and was analyzed by Illumina paired-end DNA sequencing.

    Techniques: Genome Wide, Sequencing

    Fun30 is required for normal CEN -flanking nucleosome positioning and/or CEN core particle structure. A) Genome browser trace of Fun30 ChIP enrichment and nucleosome dyad frequency centred on and surrounding yeast CEN1 . The upper trace shows Log 2 Fun30 ChIP-seq enrichment values binned at 10 bp intervals and smoothed with a 3 bin moving average. Wildtype (WT) and Δfun30 chromatin was digested with MNase and nuclease-protected DNA species sequenced using paired-end mode Illumina technology. Nucleosome sequencing data (nuc) traces were plotted as mirror images in the lower panel. The graph shows a map of the centre point positions of paired sequence reads with end-to-end distances of 150 bp+/−20% wild-type and Δfun30 mutant chromatin samples surrounding CEN1 . The frequency distributions, which effectively map chromatin particle dyads, were binned at 10 bp intervals, and smoothed by applying a 3 bin moving average. Peaks in the dyad distributions correspond to translationally-positioned nucleosomes in the original genome. The CEN core particle is also mapped using this method and can be visualised as a small peak centred on the CEN region marked with a grey box. Pink bars show the positions of ORFs (B–D) Genome browser plots of Fun30 ChIP-seq and nucleosome sequence distributions as described above for CEN10, 11 and 12 respectively. Fun30-dependent changes in the height of a nucleosome dyad or CEN core particle peak are marked with a red asterix. Fun30-dependent changes in the position of a CEN -flanking nucleosome dyad peak are marked with red arrows. Genome browser plots for all yeast CENs are shown in Figure S6 .

    Journal: PLoS Genetics

    Article Title: SWI/SNF-Like Chromatin Remodeling Factor Fun30 Supports Point Centromere Function in S. cerevisiae

    doi: 10.1371/journal.pgen.1002974

    Figure Lengend Snippet: Fun30 is required for normal CEN -flanking nucleosome positioning and/or CEN core particle structure. A) Genome browser trace of Fun30 ChIP enrichment and nucleosome dyad frequency centred on and surrounding yeast CEN1 . The upper trace shows Log 2 Fun30 ChIP-seq enrichment values binned at 10 bp intervals and smoothed with a 3 bin moving average. Wildtype (WT) and Δfun30 chromatin was digested with MNase and nuclease-protected DNA species sequenced using paired-end mode Illumina technology. Nucleosome sequencing data (nuc) traces were plotted as mirror images in the lower panel. The graph shows a map of the centre point positions of paired sequence reads with end-to-end distances of 150 bp+/−20% wild-type and Δfun30 mutant chromatin samples surrounding CEN1 . The frequency distributions, which effectively map chromatin particle dyads, were binned at 10 bp intervals, and smoothed by applying a 3 bin moving average. Peaks in the dyad distributions correspond to translationally-positioned nucleosomes in the original genome. The CEN core particle is also mapped using this method and can be visualised as a small peak centred on the CEN region marked with a grey box. Pink bars show the positions of ORFs (B–D) Genome browser plots of Fun30 ChIP-seq and nucleosome sequence distributions as described above for CEN10, 11 and 12 respectively. Fun30-dependent changes in the height of a nucleosome dyad or CEN core particle peak are marked with a red asterix. Fun30-dependent changes in the position of a CEN -flanking nucleosome dyad peak are marked with red arrows. Genome browser plots for all yeast CENs are shown in Figure S6 .

    Article Snippet: MNase digested chromatin samples processed for paired-end mode Illumina DNA sequencing.

    Techniques: Chromatin Immunoprecipitation, Sequencing, Mutagenesis

    Chromatin structure around ade6-3049 is more open than around ade6-3057 , and HRA is involved in the chromatin regulation. (A) MNase sensitivity of chromatin around ade6-3049/3057 . Indicated cells of the pat1-114 background were induced to enter meiosis by temperature-shift method, and harvested 3 hr after the induction. MNase-digested DNA was prepared by MNase (0, 20, or 30 units) treatment of chromatin fraction and subsequent purification. DNA was further cut with Sac I, fractionated on 1.2% agaraose gel, and analyzed by Southern blotting using the probe indicated by the open box. The vertical arrow and the open arrowhead show the ade6 ORF and the 3049/3057 site, respectively. The numbers on the left and the right side of the panel indicate the positions of λ/ Eco T14 I fragments used for electrophoresis marker and the positions from the first A of the ade6 ORF, respectively. The dotted lines indicate a region in which MNase-sensitive sites are clustered around ade6-3049 . Presented is an example from two independent experiments, whose results were similar to each other. (B) HRA deletion reduced acetylation level of H3K9 around ade6-3049 . Indicated cells of the pat1-114 ). DNA isolated from immunoprecipitates and whole-cell extracts was analyzed by real-time qPCR, where fragments corresponding to ade6-3049/3057 and the prp3 + promoter were amplified. Relative enrichment at ade6-3049/3057 over prp3 is shown. Bar graphs are created based on mean values of two independent experiments (shown by ○).

    Journal: Genetics

    Article Title: Correlation of Meiotic DSB Formation and Transcription Initiation Around Fission Yeast Recombination Hotspots

    doi: 10.1534/genetics.116.197954

    Figure Lengend Snippet: Chromatin structure around ade6-3049 is more open than around ade6-3057 , and HRA is involved in the chromatin regulation. (A) MNase sensitivity of chromatin around ade6-3049/3057 . Indicated cells of the pat1-114 background were induced to enter meiosis by temperature-shift method, and harvested 3 hr after the induction. MNase-digested DNA was prepared by MNase (0, 20, or 30 units) treatment of chromatin fraction and subsequent purification. DNA was further cut with Sac I, fractionated on 1.2% agaraose gel, and analyzed by Southern blotting using the probe indicated by the open box. The vertical arrow and the open arrowhead show the ade6 ORF and the 3049/3057 site, respectively. The numbers on the left and the right side of the panel indicate the positions of λ/ Eco T14 I fragments used for electrophoresis marker and the positions from the first A of the ade6 ORF, respectively. The dotted lines indicate a region in which MNase-sensitive sites are clustered around ade6-3049 . Presented is an example from two independent experiments, whose results were similar to each other. (B) HRA deletion reduced acetylation level of H3K9 around ade6-3049 . Indicated cells of the pat1-114 ). DNA isolated from immunoprecipitates and whole-cell extracts was analyzed by real-time qPCR, where fragments corresponding to ade6-3049/3057 and the prp3 + promoter were amplified. Relative enrichment at ade6-3049/3057 over prp3 is shown. Bar graphs are created based on mean values of two independent experiments (shown by ○).

    Article Snippet: Genomic DNA was treated with 0, 20, or 30 units of micrococcal nuclease (MNase) (Takara), digested with Sac I, and separated on a 1.2% agarose gel.

    Techniques: Purification, Southern Blot, Electrophoresis, Marker, Isolation, Real-time Polymerase Chain Reaction, Amplification

    Phased nucleosome arrays flanked TSSs of rice genes. (A) Nucleosome positioning profile associated with active genes. Phased nucleosome arrays are detectable after the TSSs. (B) Nucleosome positioning profile associated with non-expressed genes. Phased nucleosome arrays are detected on either side of the TSSs. (C) Distribution of DHS length for five different DHS categories. Note: the length of DHSs associated with proximal promoters (black line) are more variable than the lengths of other DHSs. (D) Heatmap of nucleosome positioning associated with active genes. Left panel: All expressed genes were sorted by the length of DHSs located in proximal promoters. The 5′ ends of the MNase-seq reads were mapped within 1 kb upstream and 1 kb downstream of the TSS of each gene to show the boundaries of nucleosomes core and linker. The red line on the left heatmap indicates the boundaries of DHSs. With the same order of the genes as in the left panel, the 5′ ends of DNase-seq reads (middle panel) and the fragments per kilobase of exon per million fragments mapped (FPKM) value log10 transformation (right panel) were mapped to show the DNase I sensitivity and the expression level of each gene, respectively.

    Journal: PLoS Genetics

    Article Title: Genome-Wide Nucleosome Positioning Is Orchestrated by Genomic Regions Associated with DNase I Hypersensitivity in Rice

    doi: 10.1371/journal.pgen.1004378

    Figure Lengend Snippet: Phased nucleosome arrays flanked TSSs of rice genes. (A) Nucleosome positioning profile associated with active genes. Phased nucleosome arrays are detectable after the TSSs. (B) Nucleosome positioning profile associated with non-expressed genes. Phased nucleosome arrays are detected on either side of the TSSs. (C) Distribution of DHS length for five different DHS categories. Note: the length of DHSs associated with proximal promoters (black line) are more variable than the lengths of other DHSs. (D) Heatmap of nucleosome positioning associated with active genes. Left panel: All expressed genes were sorted by the length of DHSs located in proximal promoters. The 5′ ends of the MNase-seq reads were mapped within 1 kb upstream and 1 kb downstream of the TSS of each gene to show the boundaries of nucleosomes core and linker. The red line on the left heatmap indicates the boundaries of DHSs. With the same order of the genes as in the left panel, the 5′ ends of DNase-seq reads (middle panel) and the fragments per kilobase of exon per million fragments mapped (FPKM) value log10 transformation (right panel) were mapped to show the DNase I sensitivity and the expression level of each gene, respectively.

    Article Snippet: Since the position of the nucleosome center (dyad), which can be identified as the middle position of each paired-end read, is not affected by different levels of MNase digestion, we can calculate the spacing of between two adjacent nucleosomes using the midway point between paired MNase-seq reads rather than 5' ends.

    Techniques: Transformation Assay, Expressing

    Nucleosome positioning profiles associated with DHSs with different lengths in proximal promoters. (A) DHSs in 320–480 bp. (B) DHSs in 200–320 bp. (C) DHSs in 140–200 bp. (D) DHSs in 80–140 bp. (E) DHSs in 20–80 bp. Y-axes show normalized reads of DNase-seq and MNase-seq. Zero on the X-axis indicates the boundary of DHSs toward short arm of the chromosomes. Black ellipses indicate the inferred nucleosomes. Grey ellipses indicate -1 nucleosomes within DHSs. Black vertical lines in (d, e) indicate the left and right boundaries of the DHSs inferred by DNase-seq reads.

    Journal: PLoS Genetics

    Article Title: Genome-Wide Nucleosome Positioning Is Orchestrated by Genomic Regions Associated with DNase I Hypersensitivity in Rice

    doi: 10.1371/journal.pgen.1004378

    Figure Lengend Snippet: Nucleosome positioning profiles associated with DHSs with different lengths in proximal promoters. (A) DHSs in 320–480 bp. (B) DHSs in 200–320 bp. (C) DHSs in 140–200 bp. (D) DHSs in 80–140 bp. (E) DHSs in 20–80 bp. Y-axes show normalized reads of DNase-seq and MNase-seq. Zero on the X-axis indicates the boundary of DHSs toward short arm of the chromosomes. Black ellipses indicate the inferred nucleosomes. Grey ellipses indicate -1 nucleosomes within DHSs. Black vertical lines in (d, e) indicate the left and right boundaries of the DHSs inferred by DNase-seq reads.

    Article Snippet: Since the position of the nucleosome center (dyad), which can be identified as the middle position of each paired-end read, is not affected by different levels of MNase digestion, we can calculate the spacing of between two adjacent nucleosomes using the midway point between paired MNase-seq reads rather than 5' ends.

    Techniques:

    Patterns of nucleosome positioning around DHSs in the rice genome. The nucleosome positioning profiles were shown around the DHSs located in (A) proximal promoters (within 200 bp upstream of a TSS); (B) distal promoters (200–1000 bp upstream of a TSS); (C) within genes; (D) downstream regions of genes (within 200 bp downstream of gene transcription); (E) intergenic regions and (F) 10,000 randomly selected genomic regions. Y-axes show normalized reads (read number in per bp genome in per million reads) within 1 kb upstream and downstream around the DHSs. Ellipses indicate the nucleosomes within (grey) and outside (black) of DHSs. Arrows in (A–D) indicate the direction of gene transcription. Single-end MNase-seq reads were used in mapping nucleosome positioning.

    Journal: PLoS Genetics

    Article Title: Genome-Wide Nucleosome Positioning Is Orchestrated by Genomic Regions Associated with DNase I Hypersensitivity in Rice

    doi: 10.1371/journal.pgen.1004378

    Figure Lengend Snippet: Patterns of nucleosome positioning around DHSs in the rice genome. The nucleosome positioning profiles were shown around the DHSs located in (A) proximal promoters (within 200 bp upstream of a TSS); (B) distal promoters (200–1000 bp upstream of a TSS); (C) within genes; (D) downstream regions of genes (within 200 bp downstream of gene transcription); (E) intergenic regions and (F) 10,000 randomly selected genomic regions. Y-axes show normalized reads (read number in per bp genome in per million reads) within 1 kb upstream and downstream around the DHSs. Ellipses indicate the nucleosomes within (grey) and outside (black) of DHSs. Arrows in (A–D) indicate the direction of gene transcription. Single-end MNase-seq reads were used in mapping nucleosome positioning.

    Article Snippet: Since the position of the nucleosome center (dyad), which can be identified as the middle position of each paired-end read, is not affected by different levels of MNase digestion, we can calculate the spacing of between two adjacent nucleosomes using the midway point between paired MNase-seq reads rather than 5' ends.

    Techniques:

    Patterns of nucleosome positioning around DHSs in the human genome. DHSs (data from CD4+ T cell line) were also divided into five different categories based on their genomic locations: (A) proximal promoters (within 200 bp upstream of a TSS); (B) within genes; and (C) intergenic regions. Y-axes show normalized MNase-seq reads (read number in per bp genome in per million reads). Zero on the x-axes indicates the most sensitive site of the aligned DHSs. Ellipses indicate phased nucleosomes with H2A.Z. Arrows in (A, B) indicate the direction of gene transcription.

    Journal: PLoS Genetics

    Article Title: Genome-Wide Nucleosome Positioning Is Orchestrated by Genomic Regions Associated with DNase I Hypersensitivity in Rice

    doi: 10.1371/journal.pgen.1004378

    Figure Lengend Snippet: Patterns of nucleosome positioning around DHSs in the human genome. DHSs (data from CD4+ T cell line) were also divided into five different categories based on their genomic locations: (A) proximal promoters (within 200 bp upstream of a TSS); (B) within genes; and (C) intergenic regions. Y-axes show normalized MNase-seq reads (read number in per bp genome in per million reads). Zero on the x-axes indicates the most sensitive site of the aligned DHSs. Ellipses indicate phased nucleosomes with H2A.Z. Arrows in (A, B) indicate the direction of gene transcription.

    Article Snippet: Since the position of the nucleosome center (dyad), which can be identified as the middle position of each paired-end read, is not affected by different levels of MNase digestion, we can calculate the spacing of between two adjacent nucleosomes using the midway point between paired MNase-seq reads rather than 5' ends.

    Techniques:

    Association IPA1-binding sites with phased nucleosomes. An example of phased nucleosome arrays that flank an intergenic IPA1-binding site on rice chromosome 8. This binding site is overlapped with a DHS (red arrow). The distribution of MNase-seq data (dyad density calculated from paired-end reads by NucleR) and DNase-seq data (density calculated by F-seq) were used to present the nucleosome and DHS positions. Phased nucleosomes and DHS regions were also schematically marked.

    Journal: PLoS Genetics

    Article Title: Genome-Wide Nucleosome Positioning Is Orchestrated by Genomic Regions Associated with DNase I Hypersensitivity in Rice

    doi: 10.1371/journal.pgen.1004378

    Figure Lengend Snippet: Association IPA1-binding sites with phased nucleosomes. An example of phased nucleosome arrays that flank an intergenic IPA1-binding site on rice chromosome 8. This binding site is overlapped with a DHS (red arrow). The distribution of MNase-seq data (dyad density calculated from paired-end reads by NucleR) and DNase-seq data (density calculated by F-seq) were used to present the nucleosome and DHS positions. Phased nucleosomes and DHS regions were also schematically marked.

    Article Snippet: Since the position of the nucleosome center (dyad), which can be identified as the middle position of each paired-end read, is not affected by different levels of MNase digestion, we can calculate the spacing of between two adjacent nucleosomes using the midway point between paired MNase-seq reads rather than 5' ends.

    Techniques: Binding Assay