Restriction Enzymes for Epigenetic Analysis (EpiMark® Validated)
Many restriction enzymes are sensitive to the DNA methylation states. Cleavage can be blocked or impaired when a particular base in the recognition site is modified. Scientists at NEB recently identified the MspJI (NEB #R0661) family of restriction enzymes, which are dependent on methylation and hydroxymethylation for cleavage to occur. These enzymes excise ~ 32 base pair fragments containing a centrally located 5-hmC or 5-mC modified residue that can be extracted and sequenced. Due to the known position of this epigenetic modification, bisulfite conversion is not required prior to downstream analysis. These EpiMark® validated, methylation-dependent restriction enzymes expand the potential for mapping epigenetic modifications and simplify the study of DNA methylation. Additionally, they provide an opportunity to better understand the role of 5-hydroxymethylcytosine in the genome.
Several of our existing restriction enzymes can also be used to study epigenetic modifications of DNA, such as DpnI (NEB #R0176) and DpnII (NEB #R0543) that recognize the same sequence, but different methylation patterns. McrBC also only cleaves DNA that is methylated cytosine on one or both strands. MspI (NEB #R0106) and HpaII (NEB #R0171) recognize the same sequence (CCGG) but are sensitive to different methylation status. HpaII cleaves only a completely unmodified site: any modification (5-mC, 5-hmCo or 5-ghmC) at either cytosine blocks cleavage. MspI will recognize and cleave 5-hmC and 5-hmC, but not 5-ghmc. These enzymes are included in the EpiMark® 5-hmC and 5-mC Analysis Kit (NEB #E3317).
Simplify DNA Methylation Analysis with MspJI
EpiMark® is a registered trademark of New England Biolabs, Inc.
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Protocols for Restriction Enzymes for Epigenetic Analysis (EpiMark® Validated)
- Protocol for Glucosylation and digestion of Genomic DNA using AbaSI (#R0665)
- Protocol for generating 32 bp fragments from modified CpG sites in genomic DNA using LpnPI (R0663)
- Protocol for generating 32 bp fragments from modified CpG sites in genomic DNA using FspEI
- Protocol for generating 32 bp fragments from modified CpG sites in genomic DNA using MspJI
- Double Digest Protocol with Standard Restriction Enzymes
- Protocol for Direct Digestion of gDNA during droplet digital PCR (ddPCR)
- Protocol for Digestion Prior to droplet digital PCR (ddPCR)
- Optimizing Restriction Endonuclease Reactions
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Epigenetics - Expanding on Genomic Foundations
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Restriction Endonucleases: Molecular Cloning and Beyond
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Epigenetics Brochure
The Epigenetics brochure provides information on these unique solutions to study DNA and histone modifications. NEB offers a suite of validated products for epigenetics research.
- Dam-Dcm and CpG Methylation
- Frequencies of Restriction Sites
- EpiMark® Methylated DNA Enrichment Kit Troubleshooting Guide
- Alteration of Apparent Recognition Specificities Using Methylases
- Dam and Dcm Methylases of E. coli
- Restriction Enzyme Tips
- Restriction of Foreign DNA by E. coli K-12
- Site Preferences
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Troubleshooting Guides
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- Mooijman D, Dey S S, Boisset JC, Crosetto N, van Oudenaarden A 2016. Single-cell 5hmC sequencing reveals chromosome-wide cell-to-cell variability and enables lineage reconstruction Nature Biotechnology. 34, PubMedID: 27347753, DOI: 10.1038/nbt.3598
Publications related to Restriction Enzymes for Epigenetic Analysis (EpiMark® Validated)
Videos
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Interactive Tutorial Explaining the Phenomenon of Epigenetics at a Molecular Level
Watch an interactive tutorial explaining the different molecular mechanisms by which epigenetic change influences gene expression. Learn about how NEB’s line of EpiMark® validated reagents are targeted to the various enzymes and DNA elements that are altered by epigenetic change.
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What Does Epigenetics Have to Do with Honeybees?
Rick Feehery, Research Associate at New England Biolabs, Inc, explains the mechanisms of epigenetic DNA modification. To drive home the power of such tiny changes, he uses the example of honeybee colonies, wherein DNA methylation is the only factor that determines whether a bee is born a worker, drone or queen.
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What are Restriction Enzymes?
Watch as Geoff Wilson, Restriction Enzymes Division Head, describes what restriction enzymes are and how they revolutionized molecular biology.
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How Complex is Epigenetics?
Epigenetic changes to DNA impact a wide range of biological processes such as organism development and disease progression. Watch as Sriharsa enthusiastically describes this exciting and complex field that has the power to "re-write" the course of DNA transcription.
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How Can Epigenetics Help Us Treat Diseases?
Cancer cells have epigenetic changes to their DNA. One of these causes the turning off (silencing) of tumor suppressor genes, a small set of genes involved in cell cycle control. Sriharsa discusses drugs currently in the clinic that are able to demethylate DNA and improve the lives of cancer patients.
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EpiMark 5-hmC and 5-mC Analysis Kit Protocol Animation
New England Biolabs is pleased to introduce the EpiMark® 5-hmC and 5-mC Analysis Kit, a simple and robust method for the identification and quantitation of 5-hydroxymethylcytosine (5-hmC) and 5-methylcytosine (5-mC) within a specific DNA locus.
EpiMark® is a registered trademark of New England Biolabs, Inc.
