mnase  (New England Biolabs)


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    Structured Review

    New England Biolabs mnase
    DAM accessibility correlates with nucleosome positions . This figure shows the superimposition of average DAM accessibility versus average <t>MNase</t> accessibility around the transcription start site (TSS) of 3,904 strongly expressed C. elegans genes. The dotted red curve represents a moving average of the muscle profile with a sliding window of 400 nucleotides. Positioned <t>H3K4me2/3</t> nucleosomes are represented by ovals above the picture of the generic gene. Numbers on the nucleosomes indicate their positions relative to the TSS. [NDR = nucleosome depleted region]
    Mnase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 92/100, based on 41 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/mnase/product/New England Biolabs
    Average 92 stars, based on 41 article reviews
    Price from $9.99 to $1999.99
    mnase - by Bioz Stars, 2020-05
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    Images

    1) Product Images from "Distributed probing of chromatin structure in vivo reveals pervasive chromatin accessibility for expressed and non-expressed genes during tissue differentiation in C. elegans"

    Article Title: Distributed probing of chromatin structure in vivo reveals pervasive chromatin accessibility for expressed and non-expressed genes during tissue differentiation in C. elegans

    Journal: BMC Genomics

    doi: 10.1186/1471-2164-11-465

    DAM accessibility correlates with nucleosome positions . This figure shows the superimposition of average DAM accessibility versus average MNase accessibility around the transcription start site (TSS) of 3,904 strongly expressed C. elegans genes. The dotted red curve represents a moving average of the muscle profile with a sliding window of 400 nucleotides. Positioned H3K4me2/3 nucleosomes are represented by ovals above the picture of the generic gene. Numbers on the nucleosomes indicate their positions relative to the TSS. [NDR = nucleosome depleted region]
    Figure Legend Snippet: DAM accessibility correlates with nucleosome positions . This figure shows the superimposition of average DAM accessibility versus average MNase accessibility around the transcription start site (TSS) of 3,904 strongly expressed C. elegans genes. The dotted red curve represents a moving average of the muscle profile with a sliding window of 400 nucleotides. Positioned H3K4me2/3 nucleosomes are represented by ovals above the picture of the generic gene. Numbers on the nucleosomes indicate their positions relative to the TSS. [NDR = nucleosome depleted region]

    Techniques Used:

    Related Articles

    Isolation:

    Article Title: Interplay between FACT subunit SPT16 and TRIM33 can remodel chromatin at macrophage distal regulatory elements
    Article Snippet: .. Micrococcal nuclease (MNase) digestion was performed on isolated nuclei with indicated concentrations of MNase (New England Biolabs) in 50 mM Tris-HCl, 5 mM CaCl2 for 10 min at 37 °C. ..

    Incubation:

    Article Title: Transcription-associated histone pruning demarcates macroH2A chromatin domains
    Article Snippet: .. 12 ul MNase (NEB) was added and the reaction was incubated at 37°C for 10 min. ..

    Article Title: Genome-Wide Transcriptional Regulation Mediated by Biochemically Distinct SWI/SNF Complexes
    Article Snippet: .. 0.5uL MNAse (NEB, 2 × 106 units/mL) was added to tubes and incubated 15 minutes at 37°C . .. MNase digestion was stopped by adding 0.1 volumes 0.5M EDTA and reactions were incubated for 5 minutes on ice.

    Article Title: SUMO polymeric chains are involved in nuclear foci formation and chromatin organization in Trypanosoma brucei procyclic forms
    Article Snippet: .. Pellets were washed [10 mM HEPES, 35 mM NaCl, 500 μM MgCl2 , 500 μM CaCl2 , 1 mM PMSF, 5.2 mM β-mercaptoethanol (Sigma)] and incubated with increasing amounts of microccocal nuclease (New England Biolabs) for 5 min at 37°C (0, 3, 7 U). ..

    Expressing:

    Article Title: Distributed probing of chromatin structure in vivo reveals pervasive chromatin accessibility for expressed and non-expressed genes during tissue differentiation in C. elegans
    Article Snippet: .. Abbreviations DALEC: Direct Asymmetric Ligation End Capture; DAM: DNA Adenine Methyltransferase; GFP: Green Fluorescent Protein; H3K4me2/3: di- or tri-methylation of lysine 4 on histone H3; MNase: micrococcal nuclease; NDR: Nucleosome Depleted Region; NEB: New England Biolabs; SAGE: Serial Analysis of Gene Expression ..

    Ligation:

    Article Title: Distributed probing of chromatin structure in vivo reveals pervasive chromatin accessibility for expressed and non-expressed genes during tissue differentiation in C. elegans
    Article Snippet: .. Abbreviations DALEC: Direct Asymmetric Ligation End Capture; DAM: DNA Adenine Methyltransferase; GFP: Green Fluorescent Protein; H3K4me2/3: di- or tri-methylation of lysine 4 on histone H3; MNase: micrococcal nuclease; NDR: Nucleosome Depleted Region; NEB: New England Biolabs; SAGE: Serial Analysis of Gene Expression ..

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    Thermolabile Proteinase K is an engineered subtilisin related serine protease that cleaves the peptide bond at the carboxyl side of aliphatic or aromatic amino acid residues and will hydrolyze a
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    New England Biolabs mnase digestion buffer
    Nucleosome positioning is altered at the TSSs of genes in Δ dim-1 strain. (A) Southern blots of <t>DNA</t> from 20-min time course micrococcal nuclease <t>(MNase)</t> digest with WT and Δ dim-1 nuclei, probed for the indicated regions; the “NCU04771up start” probe covers the intergenic promoter region of gene NCU04771, including the nucleosome-free region. Arrowheads indicate the time points (8 and 10 min) from which mono- and di-nucleosomes and intervening DNA was purified for paired-end high-throughput sequencing (below). Cartoons at right show interpretation of nucleosome patterns leading to smallest fragments. (B) Average nucleosome enrichment profiles of MNase-sequencing data from WT and Δ dim-1 strains normalized to the average signal across the 5′ end of all Neurospora genes, spanning 400 bp upstream to 600 bp downstream of the TSS; numbers below indicate the peak apices, in base pairs from the transcriptional start site (TSS) in WT and Δ dim-1 strains, and the difference in the apex position, for the +1, +2, and +3 nucleosomes. (C) Representative examples of nucleosome positions in individual genes with changed (NCU08052), or unchanged (NCU04402; dim-5 ) expression in a Δ dim-1 background. Red arrows highlight nucleosome disorder in a Δ dim-1 strain of two nucleosomes that are well-positioned in a WT strain.
    Mnase Digestion Buffer, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 94/100, based on 16 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 94 stars, based on 16 article reviews
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    92
    New England Biolabs mnase
    DNA nucleases induce NET digestion . (A) Migration profile of pure λDNA after digestion with 4 U/mL <t>DNase,</t> <t>MNase,</t> or Alu-I. (B) Alu-I, DNase, and MNase dose-effects on NET dsDNA obtained after A23187 stimulation of PMN. Incubation with the restriction enzymes lasted 20 min at 37°C. DNA migration took place in 0.8% agarose gel containing ethidium bromide.
    Mnase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 92/100, based on 41 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/mnase/product/New England Biolabs
    Average 92 stars, based on 41 article reviews
    Price from $9.99 to $1999.99
    mnase - by Bioz Stars, 2020-05
    92/100 stars
      Buy from Supplier

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    New England Biolabs mnase reaction buffer
    Characterization of the NRS sequences. ( A ) EMSA comparing binding of the <t>DNA</t> binding domain of GR to a GBS sequence flanked by either the control sequence (left) or by NRS2 (right). ( B ) DNase I accessibility assay was performed with populations of transgenic cells with stably integrated reporters as indicated. Regions of interest were analyzed by qPCR ( FKBP5 : control accessible region; IGFBP1 : control inaccessible region; integr. GBS: integrated reporter region). Results are shown as % of input remaining after DNAse I digestion ±SEM (n = 3). ( C ) Nucleosome occupancy was analyzed using micrococcal nuclease <t>(MNase)</t> assays for populations of transgenic cells with stably integrated reporters as indicated. Regions of interest were analyzed by qPCR. Integr. GBS: integrated reporter region. Results are shown as % of input remaining after MNase digestion ±SEM (n = 3).
    Mnase Reaction Buffer, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/mnase reaction buffer/product/New England Biolabs
    Average 90 stars, based on 1 article reviews
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    Image Search Results


    Nucleosome positioning is altered at the TSSs of genes in Δ dim-1 strain. (A) Southern blots of DNA from 20-min time course micrococcal nuclease (MNase) digest with WT and Δ dim-1 nuclei, probed for the indicated regions; the “NCU04771up start” probe covers the intergenic promoter region of gene NCU04771, including the nucleosome-free region. Arrowheads indicate the time points (8 and 10 min) from which mono- and di-nucleosomes and intervening DNA was purified for paired-end high-throughput sequencing (below). Cartoons at right show interpretation of nucleosome patterns leading to smallest fragments. (B) Average nucleosome enrichment profiles of MNase-sequencing data from WT and Δ dim-1 strains normalized to the average signal across the 5′ end of all Neurospora genes, spanning 400 bp upstream to 600 bp downstream of the TSS; numbers below indicate the peak apices, in base pairs from the transcriptional start site (TSS) in WT and Δ dim-1 strains, and the difference in the apex position, for the +1, +2, and +3 nucleosomes. (C) Representative examples of nucleosome positions in individual genes with changed (NCU08052), or unchanged (NCU04402; dim-5 ) expression in a Δ dim-1 background. Red arrows highlight nucleosome disorder in a Δ dim-1 strain of two nucleosomes that are well-positioned in a WT strain.

    Journal: Genetics

    Article Title: Nucleosome Positioning by an Evolutionarily Conserved Chromatin Remodeler Prevents Aberrant DNA Methylation in Neurospora

    doi: 10.1534/genetics.118.301711

    Figure Lengend Snippet: Nucleosome positioning is altered at the TSSs of genes in Δ dim-1 strain. (A) Southern blots of DNA from 20-min time course micrococcal nuclease (MNase) digest with WT and Δ dim-1 nuclei, probed for the indicated regions; the “NCU04771up start” probe covers the intergenic promoter region of gene NCU04771, including the nucleosome-free region. Arrowheads indicate the time points (8 and 10 min) from which mono- and di-nucleosomes and intervening DNA was purified for paired-end high-throughput sequencing (below). Cartoons at right show interpretation of nucleosome patterns leading to smallest fragments. (B) Average nucleosome enrichment profiles of MNase-sequencing data from WT and Δ dim-1 strains normalized to the average signal across the 5′ end of all Neurospora genes, spanning 400 bp upstream to 600 bp downstream of the TSS; numbers below indicate the peak apices, in base pairs from the transcriptional start site (TSS) in WT and Δ dim-1 strains, and the difference in the apex position, for the +1, +2, and +3 nucleosomes. (C) Representative examples of nucleosome positions in individual genes with changed (NCU08052), or unchanged (NCU04402; dim-5 ) expression in a Δ dim-1 background. Red arrows highlight nucleosome disorder in a Δ dim-1 strain of two nucleosomes that are well-positioned in a WT strain.

    Article Snippet: Nuclei containing 16 µg of DNA were adjusted to 400 µl with MNase digestion buffer, CaCl2 was added to a final concentration of 2 mM, MNase (New England Biolabs, Beverly, MA) was added to a final concentration of 0.5 unit/µl, and the reaction was carried out at 37° for 20 min. At 2-min intervals, 30 µl aliquots (corresponding to 1.2 µg of DNA) were removed and mixed with 8 µl of 100 mM EGTA to stop the reaction and stored on ice.

    Techniques: Purification, Next-Generation Sequencing, Sequencing, Expressing

    DNA nucleases induce NET digestion . (A) Migration profile of pure λDNA after digestion with 4 U/mL DNase, MNase, or Alu-I. (B) Alu-I, DNase, and MNase dose-effects on NET dsDNA obtained after A23187 stimulation of PMN. Incubation with the restriction enzymes lasted 20 min at 37°C. DNA migration took place in 0.8% agarose gel containing ethidium bromide.

    Journal: Frontiers in Immunology

    Article Title: An Improved Strategy to Recover Large Fragments of Functional Human Neutrophil Extracellular Traps

    doi: 10.3389/fimmu.2013.00166

    Figure Lengend Snippet: DNA nucleases induce NET digestion . (A) Migration profile of pure λDNA after digestion with 4 U/mL DNase, MNase, or Alu-I. (B) Alu-I, DNase, and MNase dose-effects on NET dsDNA obtained after A23187 stimulation of PMN. Incubation with the restriction enzymes lasted 20 min at 37°C. DNA migration took place in 0.8% agarose gel containing ethidium bromide.

    Article Snippet: NET digestion by nucleases In a first set of experiments, 4 μg of purified λDNA (Invitrogen) was treated with 4 U/mL DNase I (Sigma Aldrich), 4 U/mL MNase (New England BioLabs, France), or 4 U/mL Alu I (New England BioLabs) for 20 min at 37°C.

    Techniques: Migration, Incubation, Agarose Gel Electrophoresis

    Differential chromatin structure and transcription factor binding between consensus and Alu RBPJ binding sites. ( A ) Heat map of clustered reads densities for the indicated genome-wide determination or DNA sequence feature centered around RBPJ peak summits for all 28 220 RBPJ binding sites. ( B ) The same analysis as in A for the 4921 RBPJ peak summits that intersected with an Alu element within 200 bp. ( C ) Quantification of DNA ends densities for MNAse digested input, RBPJ immunoprecipitated, and DNase hypersensitive DNA for cluster 1 (without Alu) and cluster 5 (with Alu) regions.

    Journal: Nucleic Acids Research

    Article Title: RBPJ binds to consensus and methylated cis elements within phased nucleosomes and controls gene expression in human aortic smooth muscle cells in cooperation with SRF

    doi: 10.1093/nar/gky562

    Figure Lengend Snippet: Differential chromatin structure and transcription factor binding between consensus and Alu RBPJ binding sites. ( A ) Heat map of clustered reads densities for the indicated genome-wide determination or DNA sequence feature centered around RBPJ peak summits for all 28 220 RBPJ binding sites. ( B ) The same analysis as in A for the 4921 RBPJ peak summits that intersected with an Alu element within 200 bp. ( C ) Quantification of DNA ends densities for MNAse digested input, RBPJ immunoprecipitated, and DNase hypersensitive DNA for cluster 1 (without Alu) and cluster 5 (with Alu) regions.

    Article Snippet: Cells were fixed with 0.7% formaldehyde and DNA was digested by 10 ul MNAse (New England Biolabs) to an average length of 120 bp.

    Techniques: Binding Assay, Genome Wide, Sequencing, Immunoprecipitation

    Characterization of the NRS sequences. ( A ) EMSA comparing binding of the DNA binding domain of GR to a GBS sequence flanked by either the control sequence (left) or by NRS2 (right). ( B ) DNase I accessibility assay was performed with populations of transgenic cells with stably integrated reporters as indicated. Regions of interest were analyzed by qPCR ( FKBP5 : control accessible region; IGFBP1 : control inaccessible region; integr. GBS: integrated reporter region). Results are shown as % of input remaining after DNAse I digestion ±SEM (n = 3). ( C ) Nucleosome occupancy was analyzed using micrococcal nuclease (MNase) assays for populations of transgenic cells with stably integrated reporters as indicated. Regions of interest were analyzed by qPCR. Integr. GBS: integrated reporter region. Results are shown as % of input remaining after MNase digestion ±SEM (n = 3).

    Journal: Nucleic Acids Research

    Article Title: Identification and characterization of DNA sequences that prevent glucocorticoid receptor binding to nearby response elements

    doi: 10.1093/nar/gkw203

    Figure Lengend Snippet: Characterization of the NRS sequences. ( A ) EMSA comparing binding of the DNA binding domain of GR to a GBS sequence flanked by either the control sequence (left) or by NRS2 (right). ( B ) DNase I accessibility assay was performed with populations of transgenic cells with stably integrated reporters as indicated. Regions of interest were analyzed by qPCR ( FKBP5 : control accessible region; IGFBP1 : control inaccessible region; integr. GBS: integrated reporter region). Results are shown as % of input remaining after DNAse I digestion ±SEM (n = 3). ( C ) Nucleosome occupancy was analyzed using micrococcal nuclease (MNase) assays for populations of transgenic cells with stably integrated reporters as indicated. Regions of interest were analyzed by qPCR. Integr. GBS: integrated reporter region. Results are shown as % of input remaining after MNase digestion ±SEM (n = 3).

    Article Snippet: For each sample containing 0.8 μg genomic DNA in 50 μl storage buffer, an equal volume of MNase reaction buffer (50 mM Tris pH 7.4; 25 mM KCl; 2.5 mM CaCl2 ; 5 mM MgCl2 ; 12.5 % glycerol) was added containing 1 μl MNase (NEB; ∼200 kunitz) for MNase-treated samples.

    Techniques: Binding Assay, Sequencing, Transgenic Assay, Stable Transfection, Real-time Polymerase Chain Reaction