mspji  (New England Biolabs)


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    Name:
    MspJI
    Description:
    MspJI 1 000 units
    Catalog Number:
    r0661l
    Price:
    450
    Size:
    1 000 units
    Category:
    Restriction Enzymes
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    Structured Review

    New England Biolabs mspji
    MspJI
    MspJI 1 000 units
    https://www.bioz.com/result/mspji/product/New England Biolabs
    Average 96 stars, based on 19 article reviews
    Price from $9.99 to $1999.99
    mspji - by Bioz Stars, 2020-09
    96/100 stars

    Images

    1) Product Images from "Genome-wide DNA methylation profiling using the methylation-dependent restriction enzyme LpnPI"

    Article Title: Genome-wide DNA methylation profiling using the methylation-dependent restriction enzyme LpnPI

    Journal: Genome Research

    doi: 10.1101/gr.222885.117

    MeD-seq wet laboratory and bioinformatics platform. ( A ) Genomic DNA is digested with LpnPI, followed by DNA repair, adaptor ligation to 32-bp fragments, size fractionation, amplification, and sequencing. ( B ) Sequencing reads are trimmed, filtered based on the CpG sequence, and aligned to the genome. ( C ) Nucleotide frequency plotted against the position in the sequencing reads, showing enrichment of CG nucleotides around 16–17 bp from the start. ( D ) Alignment of LpnPI, MspJI, and FspEI CpG-filtered MeD-seq reads obtained using fibroblast DNA. ( E ) Sequencing read profiles of the HOXA and KCNQ1 loci obtained with fibroblast DNA using LpnPI, MspJI, and FspEI. ( F ) Pearson correlation analysis of MeD-seq read counts of TSSs for LpnPI-MspJI ( left ), LpnPI-FspEI ( middle ), and FspEI-MspJI ( right ) comparisons. ( G ) Pearson correlation analysis of read counts of TSSs for technical replicates digested with LpnPI ( left ) and MspJI ( right ).
    Figure Legend Snippet: MeD-seq wet laboratory and bioinformatics platform. ( A ) Genomic DNA is digested with LpnPI, followed by DNA repair, adaptor ligation to 32-bp fragments, size fractionation, amplification, and sequencing. ( B ) Sequencing reads are trimmed, filtered based on the CpG sequence, and aligned to the genome. ( C ) Nucleotide frequency plotted against the position in the sequencing reads, showing enrichment of CG nucleotides around 16–17 bp from the start. ( D ) Alignment of LpnPI, MspJI, and FspEI CpG-filtered MeD-seq reads obtained using fibroblast DNA. ( E ) Sequencing read profiles of the HOXA and KCNQ1 loci obtained with fibroblast DNA using LpnPI, MspJI, and FspEI. ( F ) Pearson correlation analysis of MeD-seq read counts of TSSs for LpnPI-MspJI ( left ), LpnPI-FspEI ( middle ), and FspEI-MspJI ( right ) comparisons. ( G ) Pearson correlation analysis of read counts of TSSs for technical replicates digested with LpnPI ( left ) and MspJI ( right ).

    Techniques Used: Ligation, Fractionation, Amplification, Sequencing

    2) Product Images from "Covalent Modification of Bacteriophage T4 DNA Inhibits CRISPR-Cas9"

    Article Title: Covalent Modification of Bacteriophage T4 DNA Inhibits CRISPR-Cas9

    Journal: mBio

    doi: 10.1128/mBio.00648-15

    Characterization of phage T4 DNA modification. (A) Phage T4(glc-HMC), T4(HMC), and T4(C) DNA left untreated (−) or treated with (+) restriction enzymes AluI (top), which cleaves unmodified DNA; MspJI (middle), which cleaves HMC-containing DNA; or T4 glucosyltransferase (bottom), which increases the mobility of HMC-containing DNA by the addition of glucose groups. The arrows indicate the mobility shift due to glucose attachment. (B) Analysis of phage T4 DNA modification by single-molecule sequencing. Results are summarized for each genome by mapping IPD ratios at each base for each of the T4 strains studied. The coloration of each base is shown by the key at the bottom left. The T4 nucleotide sequence runs from top to bottom for each of the four genomes. The distance each colored point is displaced from the center indicates the IPD ratio (scale at bottom; leftward for the reverse strand, rightward for the forward strand). Examples of interpulse distances (indicative of modification) are shown to the right for a short segment of the T4 genome. Bars indicate the magnitude of the IPD ratio (upward for the forward strand and downward for the reverse strand). A 5′ GATC 3′ site of DAM methylation is highlighted in yellow. (C) Violin plot showing IPD ratios of A residues at 5′ GATC 3′ sequences.
    Figure Legend Snippet: Characterization of phage T4 DNA modification. (A) Phage T4(glc-HMC), T4(HMC), and T4(C) DNA left untreated (−) or treated with (+) restriction enzymes AluI (top), which cleaves unmodified DNA; MspJI (middle), which cleaves HMC-containing DNA; or T4 glucosyltransferase (bottom), which increases the mobility of HMC-containing DNA by the addition of glucose groups. The arrows indicate the mobility shift due to glucose attachment. (B) Analysis of phage T4 DNA modification by single-molecule sequencing. Results are summarized for each genome by mapping IPD ratios at each base for each of the T4 strains studied. The coloration of each base is shown by the key at the bottom left. The T4 nucleotide sequence runs from top to bottom for each of the four genomes. The distance each colored point is displaced from the center indicates the IPD ratio (scale at bottom; leftward for the reverse strand, rightward for the forward strand). Examples of interpulse distances (indicative of modification) are shown to the right for a short segment of the T4 genome. Bars indicate the magnitude of the IPD ratio (upward for the forward strand and downward for the reverse strand). A 5′ GATC 3′ site of DAM methylation is highlighted in yellow. (C) Violin plot showing IPD ratios of A residues at 5′ GATC 3′ sequences.

    Techniques Used: Modification, Mobility Shift, Sequencing, Methylation

    3) Product Images from "C9orf72 hypermethylation protects against repeat expansion-associated pathology in ALS/FTD"

    Article Title: C9orf72 hypermethylation protects against repeat expansion-associated pathology in ALS/FTD

    Journal: Acta neuropathologica

    doi: 10.1007/s00401-014-1286-y

    Hypermethylation of the C9orf72 promoter. a Cerebellar DNA from control ( n = 8, left ) and repeat-expanded cases ( n = 8, right ) were mock digested (no enzyme) or digested with Msp I, Hpa II or MspJ I. DNA was subject to repeat primed PCR and representative
    Figure Legend Snippet: Hypermethylation of the C9orf72 promoter. a Cerebellar DNA from control ( n = 8, left ) and repeat-expanded cases ( n = 8, right ) were mock digested (no enzyme) or digested with Msp I, Hpa II or MspJ I. DNA was subject to repeat primed PCR and representative

    Techniques Used: Polymerase Chain Reaction

    4) Product Images from "Degradation of non-methylated DNA by MsPJI impairs its usefulness as epigenetic tool"

    Article Title: Degradation of non-methylated DNA by MsPJI impairs its usefulness as epigenetic tool

    Journal: bioRxiv

    doi: 10.1101/072090

    Effect of MspJI on the amplification of non-methylated DNA. PCR product of 1799 bp was incubated in the absence (lane 1) or presence (lane 2) of MspJI. Treated samples were re-amplifiied by PCR. Positive (lane 3) and negative (lane 4) controls were included.
    Figure Legend Snippet: Effect of MspJI on the amplification of non-methylated DNA. PCR product of 1799 bp was incubated in the absence (lane 1) or presence (lane 2) of MspJI. Treated samples were re-amplifiied by PCR. Positive (lane 3) and negative (lane 4) controls were included.

    Techniques Used: Amplification, Methylation, Polymerase Chain Reaction, Incubation

    Effect of MspJI treatment on the real time amplification of genomic templates. qPCR reactions were performed using murine genomic DNA digested (D) or not digested (ND) with MspJI. The target sequences contained 14 (A) or none (B) CpG sites. The curves are representative of 12 independent experiments performed in duplicates.
    Figure Legend Snippet: Effect of MspJI treatment on the real time amplification of genomic templates. qPCR reactions were performed using murine genomic DNA digested (D) or not digested (ND) with MspJI. The target sequences contained 14 (A) or none (B) CpG sites. The curves are representative of 12 independent experiments performed in duplicates.

    Techniques Used: Amplification, Real-time Polymerase Chain Reaction

    PCR amplification of IL-12b promoter gene. Genomic DNA was incubated in the absence (lanes 2 and 3) or the presence (lanes 4 and 5) of MspJI, and used as template. Positive (lane 6) and negative (lane 7) amplification controls were analyzed in parallel.
    Figure Legend Snippet: PCR amplification of IL-12b promoter gene. Genomic DNA was incubated in the absence (lanes 2 and 3) or the presence (lanes 4 and 5) of MspJI, and used as template. Positive (lane 6) and negative (lane 7) amplification controls were analyzed in parallel.

    Techniques Used: Polymerase Chain Reaction, Amplification, Incubation

    Schematic representation of the experimental design. Genomic DNA is treated with MspJI. If DNA molecules are non-methylated (left), template remains intact and can be amplified by PCR. If DNA is methylated (right), MspJI degrades template and weaker or no amplification take place. Partial methylation can be better detected by qPCR as a shift in Cq values.
    Figure Legend Snippet: Schematic representation of the experimental design. Genomic DNA is treated with MspJI. If DNA molecules are non-methylated (left), template remains intact and can be amplified by PCR. If DNA is methylated (right), MspJI degrades template and weaker or no amplification take place. Partial methylation can be better detected by qPCR as a shift in Cq values.

    Techniques Used: Methylation, Amplification, Polymerase Chain Reaction, Real-time Polymerase Chain Reaction

    Electrophoresis of genomic DNA from M. musculus or G. lamblia digested with MspJI. Lane 1: 1kb DNA ladder; lane 2 and 5: undigested DNA; lanes 3 and 6: DNA incubated with MspJI for 4 hs; lane 4: DNA incubated with MspJI for 8 hs.
    Figure Legend Snippet: Electrophoresis of genomic DNA from M. musculus or G. lamblia digested with MspJI. Lane 1: 1kb DNA ladder; lane 2 and 5: undigested DNA; lanes 3 and 6: DNA incubated with MspJI for 4 hs; lane 4: DNA incubated with MspJI for 8 hs.

    Techniques Used: Electrophoresis, Incubation

    5) Product Images from "Strand-specific single-cell methylomics reveals distinct modes of DNA demethylation dynamics during early mammalian development"

    Article Title: Strand-specific single-cell methylomics reveals distinct modes of DNA demethylation dynamics during early mammalian development

    Journal: bioRxiv

    doi: 10.1101/804526

    Schematic of scMspJI-seq. ( a ) DNA methylation maintenance can be probed using strand-specific quantification of 5mC in single cells. Cells displaying methylation maintenance have symmetric levels of 5mCpG on both DNA strands of a chromosome while loss of methylation maintenance results in asymmetric levels of 5mCpG between the two DNA strands. ( b ) Single cells isolated by FACS or manual pipetting are deposited into 384-well plates and lysed. Following protease treatment to strip off chromatin and blocking of 5hmC sites by glucosylation, MspJI is used to recognize 5mC sites and cut gDNA 16 bp downstream of the methylated cytosine. After ligating double-stranded adapters – containing a cell-specific barcode (CB, pink), a random 3 bp unique molecule identifier to label individual 5mC sites on different alleles (UMI, green), 5’ Illumina adapter (IL, blue) and T7 promoter (T7, gray) – to the fragmented gDNA, molecules from all single cells are pooled and amplified by in vitro transcription. The amplified RNA molecules are used to prepare scMspJI-seq libraries and sequenced on an Illumina platform.
    Figure Legend Snippet: Schematic of scMspJI-seq. ( a ) DNA methylation maintenance can be probed using strand-specific quantification of 5mC in single cells. Cells displaying methylation maintenance have symmetric levels of 5mCpG on both DNA strands of a chromosome while loss of methylation maintenance results in asymmetric levels of 5mCpG between the two DNA strands. ( b ) Single cells isolated by FACS or manual pipetting are deposited into 384-well plates and lysed. Following protease treatment to strip off chromatin and blocking of 5hmC sites by glucosylation, MspJI is used to recognize 5mC sites and cut gDNA 16 bp downstream of the methylated cytosine. After ligating double-stranded adapters – containing a cell-specific barcode (CB, pink), a random 3 bp unique molecule identifier to label individual 5mC sites on different alleles (UMI, green), 5’ Illumina adapter (IL, blue) and T7 promoter (T7, gray) – to the fragmented gDNA, molecules from all single cells are pooled and amplified by in vitro transcription. The amplified RNA molecules are used to prepare scMspJI-seq libraries and sequenced on an Illumina platform.

    Techniques Used: DNA Methylation Assay, Methylation, Isolation, FACS, Stripping Membranes, Blocking Assay, Amplification, In Vitro

    6) Product Images from "Heritable Epigenetic Variation among Maize Inbreds"

    Article Title: Heritable Epigenetic Variation among Maize Inbreds

    Journal: PLoS Genetics

    doi: 10.1371/journal.pgen.1002372

    Variable DNA methylation patterns in near-isogenic lines and diverse inbreds. (A) The relative DNA methylation levels in selected near-isogenic lines was tested by digestion with the methylation dependent restriction enzyme MspjI followed by qPCR. Different subsets of NILs were selected and analyzed for each of 13 DMRs. The first two columns show the data from B73 and Mo17. Open circles reflect low methylation levels and black circles indicate high methylation levels. Intermediate methylation levels are indicated by gray color. The next group of 2–7 genotypes show the data from NILs that have B73 as the recurrent parent ( > 95% of the genome) and have introgression of the Mo17 haplotype in the region containing the DMR. The variable number of genotypes tested reflects the fact that some DMR loci are have more NILs with an introgression than others. The next group of 1–3 genotypes are NILs that are primarily Mo17 but have B73 introgressed at the DMR. The next two groups provide “control” genotypes of B73-like or Mo17-like NILs that do not have an introgression at the DMR. The expected patterns for cis (local) inheritance of DNA methylation or trans (unlinked) control of DNA methylation are shown. Note that the expected pattern for trans control would include a small number of genotypes with the methylation pattern from the introgressed genotype in cases where the trans-acting locus is introgressed. (B) The same type of assays were performed on a panel of 12 diverse inbred genotypes, including two inbred teosinte lines, to monitor the frequency for the hyper- and hypo-methylated states.
    Figure Legend Snippet: Variable DNA methylation patterns in near-isogenic lines and diverse inbreds. (A) The relative DNA methylation levels in selected near-isogenic lines was tested by digestion with the methylation dependent restriction enzyme MspjI followed by qPCR. Different subsets of NILs were selected and analyzed for each of 13 DMRs. The first two columns show the data from B73 and Mo17. Open circles reflect low methylation levels and black circles indicate high methylation levels. Intermediate methylation levels are indicated by gray color. The next group of 2–7 genotypes show the data from NILs that have B73 as the recurrent parent ( > 95% of the genome) and have introgression of the Mo17 haplotype in the region containing the DMR. The variable number of genotypes tested reflects the fact that some DMR loci are have more NILs with an introgression than others. The next group of 1–3 genotypes are NILs that are primarily Mo17 but have B73 introgressed at the DMR. The next two groups provide “control” genotypes of B73-like or Mo17-like NILs that do not have an introgression at the DMR. The expected patterns for cis (local) inheritance of DNA methylation or trans (unlinked) control of DNA methylation are shown. Note that the expected pattern for trans control would include a small number of genotypes with the methylation pattern from the introgressed genotype in cases where the trans-acting locus is introgressed. (B) The same type of assays were performed on a panel of 12 diverse inbred genotypes, including two inbred teosinte lines, to monitor the frequency for the hyper- and hypo-methylated states.

    Techniques Used: DNA Methylation Assay, Methylation, Real-time Polymerase Chain Reaction

    Related Articles

    Sequencing:

    Article Title: DNA methylation analysis in malignant pheochromocytoma and paraganglioma
    Article Snippet: .. In this study, we employed two types of methylation-dependent restriction enzymes: MspJI (New England Biolabs, Beverly, MA, USA), which cleaves DNA 9 bp downstream from the m CNNR (N = A, T, G or C; R = G or C) sequence , , and FspEI (New England Biolabs), which cleaves DNA 12 bp downstream from the Cm C sequence . .. One microgram of the extracted DNA was incubated with 4 units of the appropriate two enzymes at 37 °C for 8 h in 30 μl of readymade reaction buffer (New England Biolabs) .

    Staining:

    Article Title: Complete genome and methylome analysis of Neisseria meningitidis associated with increased serogroup Y disease
    Article Snippet: .. In short, 0.5 µg genomic DNA was digested with MspJI and FspEI (New England Biolabs) according to the manufacturer's instructions, and then separated on a 20% polyacrylamide gel electrophoresis (PAGE) in 0.5x TBE buffer and stained with SYBR GOLD. .. The 30–35 bp gel fragments were excised and purified using the NEB Monarch Nucleic Acid Purification Kit (New England Biolabs).

    other:

    Article Title: Covalent Modification of Bacteriophage T4 DNA Inhibits CRISPR-Cas9
    Article Snippet: One microgram of T4(C), T4(HMC), or T4(glc-HMC) was digested with AluI (R0137s; NEB), MspJI (R0661S; NEB), or T4 phage β-glucosyltransferase (M0357S; NEB) in accordance with NEB-specified protocols.

    Article Title: Genome-wide DNA methylation profiling using the methylation-dependent restriction enzyme LpnPI
    Article Snippet: LpnPI, FspEI, and MspJI (New England Biolabs) digestions were carried out according to the manufacturer's protocol.

    Polyacrylamide Gel Electrophoresis:

    Article Title: Complete genome and methylome analysis of Neisseria meningitidis associated with increased serogroup Y disease
    Article Snippet: .. In short, 0.5 µg genomic DNA was digested with MspJI and FspEI (New England Biolabs) according to the manufacturer's instructions, and then separated on a 20% polyacrylamide gel electrophoresis (PAGE) in 0.5x TBE buffer and stained with SYBR GOLD. .. The 30–35 bp gel fragments were excised and purified using the NEB Monarch Nucleic Acid Purification Kit (New England Biolabs).

    Methylation:

    Article Title: DNA methylation analysis in malignant pheochromocytoma and paraganglioma
    Article Snippet: .. In this study, we employed two types of methylation-dependent restriction enzymes: MspJI (New England Biolabs, Beverly, MA, USA), which cleaves DNA 9 bp downstream from the m CNNR (N = A, T, G or C; R = G or C) sequence , , and FspEI (New England Biolabs), which cleaves DNA 12 bp downstream from the Cm C sequence . .. One microgram of the extracted DNA was incubated with 4 units of the appropriate two enzymes at 37 °C for 8 h in 30 μl of readymade reaction buffer (New England Biolabs) .

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    New England Biolabs mspji
    MeD-seq wet laboratory and bioinformatics platform. ( A ) Genomic DNA is digested with <t>LpnPI,</t> followed by DNA repair, adaptor ligation to 32-bp fragments, size fractionation, amplification, and sequencing. ( B ) Sequencing reads are trimmed, filtered based on the CpG sequence, and aligned to the genome. ( C ) Nucleotide frequency plotted against the position in the sequencing reads, showing enrichment of CG nucleotides around 16–17 bp from the start. ( D ) Alignment of LpnPI, <t>MspJI,</t> and FspEI CpG-filtered MeD-seq reads obtained using fibroblast DNA. ( E ) Sequencing read profiles of the HOXA and KCNQ1 loci obtained with fibroblast DNA using LpnPI, MspJI, and FspEI. ( F ) Pearson correlation analysis of MeD-seq read counts of TSSs for LpnPI-MspJI ( left ), LpnPI-FspEI ( middle ), and FspEI-MspJI ( right ) comparisons. ( G ) Pearson correlation analysis of read counts of TSSs for technical replicates digested with LpnPI ( left ) and MspJI ( right ).
    Mspji, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 96/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/mspji/product/New England Biolabs
    Average 96 stars, based on 11 article reviews
    Price from $9.99 to $1999.99
    mspji - by Bioz Stars, 2020-09
    96/100 stars
      Buy from Supplier

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    MeD-seq wet laboratory and bioinformatics platform. ( A ) Genomic DNA is digested with LpnPI, followed by DNA repair, adaptor ligation to 32-bp fragments, size fractionation, amplification, and sequencing. ( B ) Sequencing reads are trimmed, filtered based on the CpG sequence, and aligned to the genome. ( C ) Nucleotide frequency plotted against the position in the sequencing reads, showing enrichment of CG nucleotides around 16–17 bp from the start. ( D ) Alignment of LpnPI, MspJI, and FspEI CpG-filtered MeD-seq reads obtained using fibroblast DNA. ( E ) Sequencing read profiles of the HOXA and KCNQ1 loci obtained with fibroblast DNA using LpnPI, MspJI, and FspEI. ( F ) Pearson correlation analysis of MeD-seq read counts of TSSs for LpnPI-MspJI ( left ), LpnPI-FspEI ( middle ), and FspEI-MspJI ( right ) comparisons. ( G ) Pearson correlation analysis of read counts of TSSs for technical replicates digested with LpnPI ( left ) and MspJI ( right ).

    Journal: Genome Research

    Article Title: Genome-wide DNA methylation profiling using the methylation-dependent restriction enzyme LpnPI

    doi: 10.1101/gr.222885.117

    Figure Lengend Snippet: MeD-seq wet laboratory and bioinformatics platform. ( A ) Genomic DNA is digested with LpnPI, followed by DNA repair, adaptor ligation to 32-bp fragments, size fractionation, amplification, and sequencing. ( B ) Sequencing reads are trimmed, filtered based on the CpG sequence, and aligned to the genome. ( C ) Nucleotide frequency plotted against the position in the sequencing reads, showing enrichment of CG nucleotides around 16–17 bp from the start. ( D ) Alignment of LpnPI, MspJI, and FspEI CpG-filtered MeD-seq reads obtained using fibroblast DNA. ( E ) Sequencing read profiles of the HOXA and KCNQ1 loci obtained with fibroblast DNA using LpnPI, MspJI, and FspEI. ( F ) Pearson correlation analysis of MeD-seq read counts of TSSs for LpnPI-MspJI ( left ), LpnPI-FspEI ( middle ), and FspEI-MspJI ( right ) comparisons. ( G ) Pearson correlation analysis of read counts of TSSs for technical replicates digested with LpnPI ( left ) and MspJI ( right ).

    Article Snippet: LpnPI, FspEI, and MspJI (New England Biolabs) digestions were carried out according to the manufacturer's protocol.

    Techniques: Ligation, Fractionation, Amplification, Sequencing

    Characterization of phage T4 DNA modification. (A) Phage T4(glc-HMC), T4(HMC), and T4(C) DNA left untreated (−) or treated with (+) restriction enzymes AluI (top), which cleaves unmodified DNA; MspJI (middle), which cleaves HMC-containing DNA; or T4 glucosyltransferase (bottom), which increases the mobility of HMC-containing DNA by the addition of glucose groups. The arrows indicate the mobility shift due to glucose attachment. (B) Analysis of phage T4 DNA modification by single-molecule sequencing. Results are summarized for each genome by mapping IPD ratios at each base for each of the T4 strains studied. The coloration of each base is shown by the key at the bottom left. The T4 nucleotide sequence runs from top to bottom for each of the four genomes. The distance each colored point is displaced from the center indicates the IPD ratio (scale at bottom; leftward for the reverse strand, rightward for the forward strand). Examples of interpulse distances (indicative of modification) are shown to the right for a short segment of the T4 genome. Bars indicate the magnitude of the IPD ratio (upward for the forward strand and downward for the reverse strand). A 5′ GATC 3′ site of DAM methylation is highlighted in yellow. (C) Violin plot showing IPD ratios of A residues at 5′ GATC 3′ sequences.

    Journal: mBio

    Article Title: Covalent Modification of Bacteriophage T4 DNA Inhibits CRISPR-Cas9

    doi: 10.1128/mBio.00648-15

    Figure Lengend Snippet: Characterization of phage T4 DNA modification. (A) Phage T4(glc-HMC), T4(HMC), and T4(C) DNA left untreated (−) or treated with (+) restriction enzymes AluI (top), which cleaves unmodified DNA; MspJI (middle), which cleaves HMC-containing DNA; or T4 glucosyltransferase (bottom), which increases the mobility of HMC-containing DNA by the addition of glucose groups. The arrows indicate the mobility shift due to glucose attachment. (B) Analysis of phage T4 DNA modification by single-molecule sequencing. Results are summarized for each genome by mapping IPD ratios at each base for each of the T4 strains studied. The coloration of each base is shown by the key at the bottom left. The T4 nucleotide sequence runs from top to bottom for each of the four genomes. The distance each colored point is displaced from the center indicates the IPD ratio (scale at bottom; leftward for the reverse strand, rightward for the forward strand). Examples of interpulse distances (indicative of modification) are shown to the right for a short segment of the T4 genome. Bars indicate the magnitude of the IPD ratio (upward for the forward strand and downward for the reverse strand). A 5′ GATC 3′ site of DAM methylation is highlighted in yellow. (C) Violin plot showing IPD ratios of A residues at 5′ GATC 3′ sequences.

    Article Snippet: One microgram of T4(C), T4(HMC), or T4(glc-HMC) was digested with AluI (R0137s; NEB), MspJI (R0661S; NEB), or T4 phage β-glucosyltransferase (M0357S; NEB) in accordance with NEB-specified protocols.

    Techniques: Modification, Mobility Shift, Sequencing, Methylation

    Hypermethylation of the C9orf72 promoter. a Cerebellar DNA from control ( n = 8, left ) and repeat-expanded cases ( n = 8, right ) were mock digested (no enzyme) or digested with Msp I, Hpa II or MspJ I. DNA was subject to repeat primed PCR and representative

    Journal: Acta neuropathologica

    Article Title: C9orf72 hypermethylation protects against repeat expansion-associated pathology in ALS/FTD

    doi: 10.1007/s00401-014-1286-y

    Figure Lengend Snippet: Hypermethylation of the C9orf72 promoter. a Cerebellar DNA from control ( n = 8, left ) and repeat-expanded cases ( n = 8, right ) were mock digested (no enzyme) or digested with Msp I, Hpa II or MspJ I. DNA was subject to repeat primed PCR and representative

    Article Snippet: DNA (1 μg) from post-mortem cerebellar tissue was restriction enzyme digested for 4 h with Hpa II (10 U), Msp I (10 U), or MspJ I (4 U) (New England Biolabs) at 37°C followed by phenol:chloroform:isoamyl alcohol extraction.

    Techniques: Polymerase Chain Reaction

    Effect of MspJI on the amplification of non-methylated DNA. PCR product of 1799 bp was incubated in the absence (lane 1) or presence (lane 2) of MspJI. Treated samples were re-amplifiied by PCR. Positive (lane 3) and negative (lane 4) controls were included.

    Journal: bioRxiv

    Article Title: Degradation of non-methylated DNA by MsPJI impairs its usefulness as epigenetic tool

    doi: 10.1101/072090

    Figure Lengend Snippet: Effect of MspJI on the amplification of non-methylated DNA. PCR product of 1799 bp was incubated in the absence (lane 1) or presence (lane 2) of MspJI. Treated samples were re-amplifiied by PCR. Positive (lane 3) and negative (lane 4) controls were included.

    Article Snippet: Digestion with MspJIGenomic DNA (1µg) was digested following the manufacturer instructions, using 2 unit of MspJI (New England Biolabs) in the presence of 1 µl double-stranded DNA activator in a 30-µL volume.

    Techniques: Amplification, Methylation, Polymerase Chain Reaction, Incubation

    Effect of MspJI treatment on the real time amplification of genomic templates. qPCR reactions were performed using murine genomic DNA digested (D) or not digested (ND) with MspJI. The target sequences contained 14 (A) or none (B) CpG sites. The curves are representative of 12 independent experiments performed in duplicates.

    Journal: bioRxiv

    Article Title: Degradation of non-methylated DNA by MsPJI impairs its usefulness as epigenetic tool

    doi: 10.1101/072090

    Figure Lengend Snippet: Effect of MspJI treatment on the real time amplification of genomic templates. qPCR reactions were performed using murine genomic DNA digested (D) or not digested (ND) with MspJI. The target sequences contained 14 (A) or none (B) CpG sites. The curves are representative of 12 independent experiments performed in duplicates.

    Article Snippet: Digestion with MspJIGenomic DNA (1µg) was digested following the manufacturer instructions, using 2 unit of MspJI (New England Biolabs) in the presence of 1 µl double-stranded DNA activator in a 30-µL volume.

    Techniques: Amplification, Real-time Polymerase Chain Reaction

    PCR amplification of IL-12b promoter gene. Genomic DNA was incubated in the absence (lanes 2 and 3) or the presence (lanes 4 and 5) of MspJI, and used as template. Positive (lane 6) and negative (lane 7) amplification controls were analyzed in parallel.

    Journal: bioRxiv

    Article Title: Degradation of non-methylated DNA by MsPJI impairs its usefulness as epigenetic tool

    doi: 10.1101/072090

    Figure Lengend Snippet: PCR amplification of IL-12b promoter gene. Genomic DNA was incubated in the absence (lanes 2 and 3) or the presence (lanes 4 and 5) of MspJI, and used as template. Positive (lane 6) and negative (lane 7) amplification controls were analyzed in parallel.

    Article Snippet: Digestion with MspJIGenomic DNA (1µg) was digested following the manufacturer instructions, using 2 unit of MspJI (New England Biolabs) in the presence of 1 µl double-stranded DNA activator in a 30-µL volume.

    Techniques: Polymerase Chain Reaction, Amplification, Incubation

    Schematic representation of the experimental design. Genomic DNA is treated with MspJI. If DNA molecules are non-methylated (left), template remains intact and can be amplified by PCR. If DNA is methylated (right), MspJI degrades template and weaker or no amplification take place. Partial methylation can be better detected by qPCR as a shift in Cq values.

    Journal: bioRxiv

    Article Title: Degradation of non-methylated DNA by MsPJI impairs its usefulness as epigenetic tool

    doi: 10.1101/072090

    Figure Lengend Snippet: Schematic representation of the experimental design. Genomic DNA is treated with MspJI. If DNA molecules are non-methylated (left), template remains intact and can be amplified by PCR. If DNA is methylated (right), MspJI degrades template and weaker or no amplification take place. Partial methylation can be better detected by qPCR as a shift in Cq values.

    Article Snippet: Digestion with MspJIGenomic DNA (1µg) was digested following the manufacturer instructions, using 2 unit of MspJI (New England Biolabs) in the presence of 1 µl double-stranded DNA activator in a 30-µL volume.

    Techniques: Methylation, Amplification, Polymerase Chain Reaction, Real-time Polymerase Chain Reaction

    Electrophoresis of genomic DNA from M. musculus or G. lamblia digested with MspJI. Lane 1: 1kb DNA ladder; lane 2 and 5: undigested DNA; lanes 3 and 6: DNA incubated with MspJI for 4 hs; lane 4: DNA incubated with MspJI for 8 hs.

    Journal: bioRxiv

    Article Title: Degradation of non-methylated DNA by MsPJI impairs its usefulness as epigenetic tool

    doi: 10.1101/072090

    Figure Lengend Snippet: Electrophoresis of genomic DNA from M. musculus or G. lamblia digested with MspJI. Lane 1: 1kb DNA ladder; lane 2 and 5: undigested DNA; lanes 3 and 6: DNA incubated with MspJI for 4 hs; lane 4: DNA incubated with MspJI for 8 hs.

    Article Snippet: Digestion with MspJIGenomic DNA (1µg) was digested following the manufacturer instructions, using 2 unit of MspJI (New England Biolabs) in the presence of 1 µl double-stranded DNA activator in a 30-µL volume.

    Techniques: Electrophoresis, Incubation