Epigenetic Analysis (Epimark® Validated)
The EpiMark® line of products from New England Biolabs is designed to simplify DNA methylation and hydroxymethylation detection and analysis, as well as ChIP, histone and nucleosome analysis. This growing line of reagents and kits includes:
- EpiMark® Methylated DNA Enrichment Kit (NEB #E2600) to enrich double-stranded methyl-CpG from fragmented genomic DNA with as little as 5 ng of input DNA
- EpiMark® Bisulfite Conversion Kit (NEB #E3318) to detect methylated cytosine via the conversion of unmodified cytosines to uracil
- EpiMark® Hot Start Taq DNA Polymerase (NEB #M0490) to amplifiy bisulfite-treated samples
- EpiMark® 5-mC and 5-hmC Analysis Kit (NEB #E3317) to identify and quantify 5-hydroxymethylcytosine at specific loci
- EpiMark® Nucleosome Assembly Kit (NEB #E5350) to prepare recombinant nucleosomes
- NEBNext® Ultra II DNA Library Prep Kit for Illumina® (NEB #E7645) to prepare Chromatin immunoprecipitated DNA samples for next-generation sequencing
EpiMark® and NEBNext® are registered trademarks of New England Biolabs, Inc.
Illumina® is a registered trademark of Illumina, Inc.
SOLiD™ is a trademark of Life Technologies, Inc.
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Protocols for Epigenetic Analysis (Epimark® Validated)
- Protocol for use with NEBNext ChIP-Seq Library Prep Reagent Set for Illumina (E6200)
- Cycling Protocol Using EpiMark™ Bisulfite Conversion Kit (E3318)
- Reagent Preparation Using EpiMark® Bisulfite Conversion Kit (E3318)
- Prebind MBD2a-Fc to Protein A Magnetic Beads (E2600)
- Wash Off Unbound DNA (E2600)
- Capture and Elute Step for Control DNA (E2600)
- Capture Methylated CpG DNA (E2600)
- Downstream Analysis (E2600)
- DNA Fragmentation (E2600)
- End-point PCR Using EpiMark Bisulfite Conversion Kit (E3318)
- Elute Captured Methylated CpG DNA (E2600)
- EpiMark® Hot Start Taq DNA Polymerase Guidelines for PCR (M0490)
- Dialysis Assembly Protocol (E5350)
- Dilution Assembly Protocol (E5350)
- Introduction (E5350)
- Gel Shift Assay for EpiMark™ Nucleosome Assembly Kit (E5350)
- DNA Concentration Formulas for EpiMark™ Nucleosome Assembly Kit (E5350)
- EpiMark™ Nucleosome Assembly Kit (E5350)
- 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)
- Reaction Protocol for EpiMark® 5-hmC and 5-mC Analysis Kit (E3317)
- Protocol for generating 32 bp fragments from modified CpG sites in genomic DNA using MspJI
- Protocol for Direct Digestion of gDNA during droplet digital PCR (ddPCR)
- Protocol for Digestion Prior to droplet digital PCR (ddPCR)
- Optimizing Restriction Endonuclease Reactions
- Double Digest Protocol with Standard Restriction Enzymes
Types of Histone Modifications
| Amino Acid | Modification |
|---|---|
| Lysine | Methylation, Acetylation, Ubiquitination, Sumoylation, ADP-Ribosylation |
| Arginine | Methylation |
| Serine | Phosphorylation |
| Threonine | Phosphorylation |
Types of DNA Modifications
References
- Kim, J.K., Samaranayake, M. and Pradhan S. (2009) Cell. Mol. Life Sci. 66, 596-612. PMID: 18985277
- Vanyushin, B.F. (2006) Curr. Top. Microbiol. Immunol. 301, 67-122. PMID: 16570846
- Mosher, R.A., Melnyk, C.W. (2010) Trends Plant Sci. 15, 204-210. PMID: 20129810
- Lyko, F., Beisel, C., Marhold, J., Paro, R. (2006) Curr. Top. Microbiol. Immunol. 310, 23-44. PMID: 16909905
- Selker, E.U., Freitag, M., Kothe, G.O., et al. (2002) Proc. Natl. Acad. Sci. U S A. 99, Suppl 4, 16485-16490. PMID: 12189210
- Kriaucionis, S. and Heintz, N. (2009) Science 324, 929-930. PMID: 19372393
- Tahiliani, M., Koh, K. P., Shen, Y., et al. (2009) Science 324, 930-935. PMID: 19372391
- Ehrlich, M., Wilson, G.G., Kuo, K.C., And Gehrke, C.W. (1987) J. Bacteriol. 169, 939-943. PMID: 3029036
- Svadbina, I.V., Zelinskaya, N.V., Kovalevskaya, N.P., Zheleznaya, L.A. and Matvienko, N.I. (2004) Biochem. (Moscow) 69, 299-305. PMID: 15061697
- Ratel, D., Ravanat, J-L., Berger, F. and Wion D. (2006) Bioessays 28, 309-315. PMID: 16479578
- Marinus, M.G. and Casadesus, J. (2009) FEMS Microbiol. Rev. 33, 488-503. PMID: 19175412
ChIP-Seq Library Construction Workflow
Videos
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What Is Epigenetics?
If all cells are created from the same genetic material, why are there so many different cell types? Listen to Sriharsa Pradhan, Senior Scientist, RNA Biology at NEB, as he describes how DNA is methylated and how this affects the path of reading the DNA code the same way an obstruction would derail a train off its tracks.
