gpc methyltransferase treatment  (New England Biolabs)


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    New England Biolabs gpc methyltransferase treatment
    DNA methylation is neutral to chromatin accessibility at the majority of cis -regulatory elements. (A) Single locus example of the heterogeneity in DNA methylation (5mC) levels at enhancers and promoters when resolved on individual molecules. Upper panel: Genome browser track displaying the chromatin marks and the average methylation as measured by Whole Genome Bisulfite Sequencing (WGBS) around the Macf1 promoter and its intragenic enhancer. Lower panel: At the molecular level, 5mC at enhancers is heterogeneous. 5mC of individual CpGs (red) is shown at molecular level (blue methylated, white unmethylated). (B) Schematic representation of the experimental strategy used to identify molecular antagonisms between 5mC and chromatin accessibility (CA). Single molecule footprinting (SMF) is performed using the <t>methyltransferase</t> M.CviPI to measure CA in the <t>GpC</t> dinucleotide context, that is distinct from the endogenous 5mC in CpG context. Bisulfite sequencing of the DNA provides continuous information on CA and 5mC over 300 bp long DNA molecules. The accessibility of each molecule is calculated using the methylation of GpCs within the 100 bp surrounding a CpG. The average accessibility is used to classify DNA molecules into accessible and inaccessible fractions. In both fractions, the average 5mC levels are calculated. White/blue lollipops represent the endogenous un-/methylated state, white/black lollipops represent the CA as measured by SMF. (C) Most intermediately methylated CpGs show no difference in 5mC between the two separated CA fractions. Violin bar plots showing the CA (top) and 5mC (bottom) at CpGs in bulk and in the two separated fractions (n = 97,808). Boxplots show median (black middle line), 25th and 75th percentiles (black boundaries). (D) Single locus example of the 5mC and CA of individual molecules at a neutral CpG. Upper panel: Genome browser track displaying the chromatin marks and the average methylation as measured by WGBS around an intergenic enhancer. Middle panel: Depicted is the average SMF signal (1 methylation %) of individual GpCs (black dots) and endogenous 5mC of individual CpGs (blue diamonds). Lower panels: Depicted are the single DNA molecules mapped to this genomic locus sorted by CA into an accessible (grey) and an inaccessible (black) fraction, and the 5mC of the molecules in both fractions. In the lower left panel, every column is a single GpC dinucleotide depicting its accessibility status (grey: accessible, black: inaccessible). In the lower right panel, every column is a single CpG dinucleotide depicting its methylation status (light blue: unmethylated, dark blue: methylated). Percentages represent average 5mC of the CpG of interest at the center in each fraction. The number of single DNA molecules used for the analysis is indicated.
    Gpc Methyltransferase Treatment, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 94 stars, based on 1 article reviews
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    gpc methyltransferase treatment - by Bioz Stars, 2022-07
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    1) Product Images from "Single molecule multi-omics reveals context-dependent regulation of enhancers by DNA methylation"

    Article Title: Single molecule multi-omics reveals context-dependent regulation of enhancers by DNA methylation

    Journal: bioRxiv

    doi: 10.1101/2022.05.19.492653

    DNA methylation is neutral to chromatin accessibility at the majority of cis -regulatory elements. (A) Single locus example of the heterogeneity in DNA methylation (5mC) levels at enhancers and promoters when resolved on individual molecules. Upper panel: Genome browser track displaying the chromatin marks and the average methylation as measured by Whole Genome Bisulfite Sequencing (WGBS) around the Macf1 promoter and its intragenic enhancer. Lower panel: At the molecular level, 5mC at enhancers is heterogeneous. 5mC of individual CpGs (red) is shown at molecular level (blue methylated, white unmethylated). (B) Schematic representation of the experimental strategy used to identify molecular antagonisms between 5mC and chromatin accessibility (CA). Single molecule footprinting (SMF) is performed using the methyltransferase M.CviPI to measure CA in the GpC dinucleotide context, that is distinct from the endogenous 5mC in CpG context. Bisulfite sequencing of the DNA provides continuous information on CA and 5mC over 300 bp long DNA molecules. The accessibility of each molecule is calculated using the methylation of GpCs within the 100 bp surrounding a CpG. The average accessibility is used to classify DNA molecules into accessible and inaccessible fractions. In both fractions, the average 5mC levels are calculated. White/blue lollipops represent the endogenous un-/methylated state, white/black lollipops represent the CA as measured by SMF. (C) Most intermediately methylated CpGs show no difference in 5mC between the two separated CA fractions. Violin bar plots showing the CA (top) and 5mC (bottom) at CpGs in bulk and in the two separated fractions (n = 97,808). Boxplots show median (black middle line), 25th and 75th percentiles (black boundaries). (D) Single locus example of the 5mC and CA of individual molecules at a neutral CpG. Upper panel: Genome browser track displaying the chromatin marks and the average methylation as measured by WGBS around an intergenic enhancer. Middle panel: Depicted is the average SMF signal (1 methylation %) of individual GpCs (black dots) and endogenous 5mC of individual CpGs (blue diamonds). Lower panels: Depicted are the single DNA molecules mapped to this genomic locus sorted by CA into an accessible (grey) and an inaccessible (black) fraction, and the 5mC of the molecules in both fractions. In the lower left panel, every column is a single GpC dinucleotide depicting its accessibility status (grey: accessible, black: inaccessible). In the lower right panel, every column is a single CpG dinucleotide depicting its methylation status (light blue: unmethylated, dark blue: methylated). Percentages represent average 5mC of the CpG of interest at the center in each fraction. The number of single DNA molecules used for the analysis is indicated.
    Figure Legend Snippet: DNA methylation is neutral to chromatin accessibility at the majority of cis -regulatory elements. (A) Single locus example of the heterogeneity in DNA methylation (5mC) levels at enhancers and promoters when resolved on individual molecules. Upper panel: Genome browser track displaying the chromatin marks and the average methylation as measured by Whole Genome Bisulfite Sequencing (WGBS) around the Macf1 promoter and its intragenic enhancer. Lower panel: At the molecular level, 5mC at enhancers is heterogeneous. 5mC of individual CpGs (red) is shown at molecular level (blue methylated, white unmethylated). (B) Schematic representation of the experimental strategy used to identify molecular antagonisms between 5mC and chromatin accessibility (CA). Single molecule footprinting (SMF) is performed using the methyltransferase M.CviPI to measure CA in the GpC dinucleotide context, that is distinct from the endogenous 5mC in CpG context. Bisulfite sequencing of the DNA provides continuous information on CA and 5mC over 300 bp long DNA molecules. The accessibility of each molecule is calculated using the methylation of GpCs within the 100 bp surrounding a CpG. The average accessibility is used to classify DNA molecules into accessible and inaccessible fractions. In both fractions, the average 5mC levels are calculated. White/blue lollipops represent the endogenous un-/methylated state, white/black lollipops represent the CA as measured by SMF. (C) Most intermediately methylated CpGs show no difference in 5mC between the two separated CA fractions. Violin bar plots showing the CA (top) and 5mC (bottom) at CpGs in bulk and in the two separated fractions (n = 97,808). Boxplots show median (black middle line), 25th and 75th percentiles (black boundaries). (D) Single locus example of the 5mC and CA of individual molecules at a neutral CpG. Upper panel: Genome browser track displaying the chromatin marks and the average methylation as measured by WGBS around an intergenic enhancer. Middle panel: Depicted is the average SMF signal (1 methylation %) of individual GpCs (black dots) and endogenous 5mC of individual CpGs (blue diamonds). Lower panels: Depicted are the single DNA molecules mapped to this genomic locus sorted by CA into an accessible (grey) and an inaccessible (black) fraction, and the 5mC of the molecules in both fractions. In the lower left panel, every column is a single GpC dinucleotide depicting its accessibility status (grey: accessible, black: inaccessible). In the lower right panel, every column is a single CpG dinucleotide depicting its methylation status (light blue: unmethylated, dark blue: methylated). Percentages represent average 5mC of the CpG of interest at the center in each fraction. The number of single DNA molecules used for the analysis is indicated.

    Techniques Used: DNA Methylation Assay, Methylation, Methylation Sequencing, Footprinting, Gel Permeation Chromatography

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    New England Biolabs gpc methyltransferase treatment
    DNA methylation is neutral to chromatin accessibility at the majority of cis -regulatory elements. (A) Single locus example of the heterogeneity in DNA methylation (5mC) levels at enhancers and promoters when resolved on individual molecules. Upper panel: Genome browser track displaying the chromatin marks and the average methylation as measured by Whole Genome Bisulfite Sequencing (WGBS) around the Macf1 promoter and its intragenic enhancer. Lower panel: At the molecular level, 5mC at enhancers is heterogeneous. 5mC of individual CpGs (red) is shown at molecular level (blue methylated, white unmethylated). (B) Schematic representation of the experimental strategy used to identify molecular antagonisms between 5mC and chromatin accessibility (CA). Single molecule footprinting (SMF) is performed using the <t>methyltransferase</t> M.CviPI to measure CA in the <t>GpC</t> dinucleotide context, that is distinct from the endogenous 5mC in CpG context. Bisulfite sequencing of the DNA provides continuous information on CA and 5mC over 300 bp long DNA molecules. The accessibility of each molecule is calculated using the methylation of GpCs within the 100 bp surrounding a CpG. The average accessibility is used to classify DNA molecules into accessible and inaccessible fractions. In both fractions, the average 5mC levels are calculated. White/blue lollipops represent the endogenous un-/methylated state, white/black lollipops represent the CA as measured by SMF. (C) Most intermediately methylated CpGs show no difference in 5mC between the two separated CA fractions. Violin bar plots showing the CA (top) and 5mC (bottom) at CpGs in bulk and in the two separated fractions (n = 97,808). Boxplots show median (black middle line), 25th and 75th percentiles (black boundaries). (D) Single locus example of the 5mC and CA of individual molecules at a neutral CpG. Upper panel: Genome browser track displaying the chromatin marks and the average methylation as measured by WGBS around an intergenic enhancer. Middle panel: Depicted is the average SMF signal (1 methylation %) of individual GpCs (black dots) and endogenous 5mC of individual CpGs (blue diamonds). Lower panels: Depicted are the single DNA molecules mapped to this genomic locus sorted by CA into an accessible (grey) and an inaccessible (black) fraction, and the 5mC of the molecules in both fractions. In the lower left panel, every column is a single GpC dinucleotide depicting its accessibility status (grey: accessible, black: inaccessible). In the lower right panel, every column is a single CpG dinucleotide depicting its methylation status (light blue: unmethylated, dark blue: methylated). Percentages represent average 5mC of the CpG of interest at the center in each fraction. The number of single DNA molecules used for the analysis is indicated.
    Gpc Methyltransferase Treatment, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/gpc methyltransferase treatment/product/New England Biolabs
    Average 94 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    gpc methyltransferase treatment - by Bioz Stars, 2022-07
    94/100 stars
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    DNA methylation is neutral to chromatin accessibility at the majority of cis -regulatory elements. (A) Single locus example of the heterogeneity in DNA methylation (5mC) levels at enhancers and promoters when resolved on individual molecules. Upper panel: Genome browser track displaying the chromatin marks and the average methylation as measured by Whole Genome Bisulfite Sequencing (WGBS) around the Macf1 promoter and its intragenic enhancer. Lower panel: At the molecular level, 5mC at enhancers is heterogeneous. 5mC of individual CpGs (red) is shown at molecular level (blue methylated, white unmethylated). (B) Schematic representation of the experimental strategy used to identify molecular antagonisms between 5mC and chromatin accessibility (CA). Single molecule footprinting (SMF) is performed using the methyltransferase M.CviPI to measure CA in the GpC dinucleotide context, that is distinct from the endogenous 5mC in CpG context. Bisulfite sequencing of the DNA provides continuous information on CA and 5mC over 300 bp long DNA molecules. The accessibility of each molecule is calculated using the methylation of GpCs within the 100 bp surrounding a CpG. The average accessibility is used to classify DNA molecules into accessible and inaccessible fractions. In both fractions, the average 5mC levels are calculated. White/blue lollipops represent the endogenous un-/methylated state, white/black lollipops represent the CA as measured by SMF. (C) Most intermediately methylated CpGs show no difference in 5mC between the two separated CA fractions. Violin bar plots showing the CA (top) and 5mC (bottom) at CpGs in bulk and in the two separated fractions (n = 97,808). Boxplots show median (black middle line), 25th and 75th percentiles (black boundaries). (D) Single locus example of the 5mC and CA of individual molecules at a neutral CpG. Upper panel: Genome browser track displaying the chromatin marks and the average methylation as measured by WGBS around an intergenic enhancer. Middle panel: Depicted is the average SMF signal (1 methylation %) of individual GpCs (black dots) and endogenous 5mC of individual CpGs (blue diamonds). Lower panels: Depicted are the single DNA molecules mapped to this genomic locus sorted by CA into an accessible (grey) and an inaccessible (black) fraction, and the 5mC of the molecules in both fractions. In the lower left panel, every column is a single GpC dinucleotide depicting its accessibility status (grey: accessible, black: inaccessible). In the lower right panel, every column is a single CpG dinucleotide depicting its methylation status (light blue: unmethylated, dark blue: methylated). Percentages represent average 5mC of the CpG of interest at the center in each fraction. The number of single DNA molecules used for the analysis is indicated.

    Journal: bioRxiv

    Article Title: Single molecule multi-omics reveals context-dependent regulation of enhancers by DNA methylation

    doi: 10.1101/2022.05.19.492653

    Figure Lengend Snippet: DNA methylation is neutral to chromatin accessibility at the majority of cis -regulatory elements. (A) Single locus example of the heterogeneity in DNA methylation (5mC) levels at enhancers and promoters when resolved on individual molecules. Upper panel: Genome browser track displaying the chromatin marks and the average methylation as measured by Whole Genome Bisulfite Sequencing (WGBS) around the Macf1 promoter and its intragenic enhancer. Lower panel: At the molecular level, 5mC at enhancers is heterogeneous. 5mC of individual CpGs (red) is shown at molecular level (blue methylated, white unmethylated). (B) Schematic representation of the experimental strategy used to identify molecular antagonisms between 5mC and chromatin accessibility (CA). Single molecule footprinting (SMF) is performed using the methyltransferase M.CviPI to measure CA in the GpC dinucleotide context, that is distinct from the endogenous 5mC in CpG context. Bisulfite sequencing of the DNA provides continuous information on CA and 5mC over 300 bp long DNA molecules. The accessibility of each molecule is calculated using the methylation of GpCs within the 100 bp surrounding a CpG. The average accessibility is used to classify DNA molecules into accessible and inaccessible fractions. In both fractions, the average 5mC levels are calculated. White/blue lollipops represent the endogenous un-/methylated state, white/black lollipops represent the CA as measured by SMF. (C) Most intermediately methylated CpGs show no difference in 5mC between the two separated CA fractions. Violin bar plots showing the CA (top) and 5mC (bottom) at CpGs in bulk and in the two separated fractions (n = 97,808). Boxplots show median (black middle line), 25th and 75th percentiles (black boundaries). (D) Single locus example of the 5mC and CA of individual molecules at a neutral CpG. Upper panel: Genome browser track displaying the chromatin marks and the average methylation as measured by WGBS around an intergenic enhancer. Middle panel: Depicted is the average SMF signal (1 methylation %) of individual GpCs (black dots) and endogenous 5mC of individual CpGs (blue diamonds). Lower panels: Depicted are the single DNA molecules mapped to this genomic locus sorted by CA into an accessible (grey) and an inaccessible (black) fraction, and the 5mC of the molecules in both fractions. In the lower left panel, every column is a single GpC dinucleotide depicting its accessibility status (grey: accessible, black: inaccessible). In the lower right panel, every column is a single CpG dinucleotide depicting its methylation status (light blue: unmethylated, dark blue: methylated). Percentages represent average 5mC of the CpG of interest at the center in each fraction. The number of single DNA molecules used for the analysis is indicated.

    Article Snippet: For the GpC methyltransferase treatment, freshly made GpC methyltransferase mix (1x M.GpC buffer, 300 mM sucrose, 64 µM SAM (NEB, #B9003S)) and 200 U M.CviPI (NEB, #M0227L) were added and incubated at 37°C for 7.5 min. For a second incubation round at 37°C for 7.5 min the reaction was replenished with 100U of M.CviPI and 128 pmol of SAM.

    Techniques: DNA Methylation Assay, Methylation, Methylation Sequencing, Footprinting, Gel Permeation Chromatography