Base Modifying Enzymes
NEB offers a selection of base modifying enzymes.
Methyltransferases
DNA methyltransferases are base modifying enzymes that transfer a methyl group from S-adenosylmethionine to either adenine or cytosine residues and can be used to generate methylated DNA at specific sites for gene expression studies. Our selection includes CpG methyltransferase (NEB #M0226), which transfers a methyl group to the C5 position of cytosine residues and is especially useful for studying CpG methylation effects. Several protein methyltransferases are also available for the specific methylation of lysine and arginine residues in Histone H3 and H4 for gene regulation studies.
Deaminases
DNA Deaminases are base modifying enzymes that remove an amino group from nucleotides in DNA. Different types of deaminases act on different DNA bases. Adenosine deaminases deaminate adenosine to form inosine. Guanine deaminases deaminate guanine to form xanthosine. They are useful in base editing technologies and other applications. Our selection of deaminases includes APOBEC3A (NEB #M0648), a cytidine deaminase, that catalyzes the deamination of cytosine or 5-methylcytosine in single-stranded DNA to produce either uracil or thymine.
Demethylases
DNA Demethylases are base modifying enzymes that remove methyl groups from DNA. DNA demethylation can occur passively (if methylation status is not maintained during DNA replication) or actively (enzymatic demethylation). They are useful in enabling enzymatic strategies for sensitive detection of epigenetic modifications. NEB offers TET2 (NEB #M1524), a ten-eleven translocation protein, that plays a crucial role in DNA demethylation by oxidizing 5-methylcytosine (5mC), a key epigenetic marker, in a stepwise manner to 5-hydroxymethylcytosine (5hmC), then 5-formylcytosine (5fC) and finally to 5-carboxycytosine (5caC).
NEB offers a selection of DNA and protein methyltransferases.
NEB offers a selection of base modifying enzymes.
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Epigenetics - Expanding on Genomic Foundations
- Epigenetics Brochure
- EpiMark® Methylated DNA Enrichment Kit Troubleshooting Guide
- Dam and Dcm Methylases of E. coli
Feature Articles
Brochures
Troubleshooting Guides
Usage Guidelines
- Pirone-Davies, C., Hoffmann, M., Roberts, R.J., Muruvanda, T., Timme, R.E., Strain, E., Luo, Y., Payne, J., Luong, K., Song, Y., Tsai, Y.C., Boitano, M., Clark, T.A., Korlach, J., Evans, P.S., Allard, M.W. (2015) Genome-Wide Methylation Patterns in Salmonella enterica Subsp. enterica Serovars PLoS One; 10(4), e0123639. PubMedID: 25860355
- Seib, K.L., Jen, F.E., Tan, A., Scott, A.L., Kumar, R., Power, P.M., Chen, L.T., Wu, H.J., Wang, A.H., Hill, D.M., Luyten, Y.A., Morgan, R.D., Roberts, R.J., Maiden, M.C., Boitano, M., Clark, T.A., Korlach, J., Rao, D.N. and Jennings, M.P. (2015) Specificity of the ModAll, ModA12 and ModD1 epigenetic regulator N6-adenine DNA methyltransferases of Neisseria Meningitidis Nucleic Acids Res; 43(8), 4150-4162. PubMedID: 25845594, DOI: 10.1093/nar/gkv219
- Roberts, R.J., Vincze, T., Posfai, J., Macelis, D. (2015) REBASE - A database for DNA restriction and modification: enzymes, genes and genomes Nucleic Acids Res; 43, D298-D299. PubMedID: 25378308
- Fomenkov, A., Lunnen, K.D., Zhu, Z., Anton, B.P., Wilson, G.G., Vincze, T. and Roberts, R.J. (2015) Complete genome sequence and methylome analysis of bacillus strain x1 Genome Announc; 3(1), PubMedID: 25700417
- Anton, B.P., Mongodin, E.F., Agrawal, S., Fomenkov, A., Byrd, D.R., Roberts, R.J. and Raleigh, E.A. (2015) Complete Genome Sequence of ER2796, a DNA Methyltransferase-Deficient Strain of Escherichia coli K-12 PLoS One; 10(5), e0127446. PubMedID: 26010885
- Xu, S-Y., Boitano, M., Clark, T.A., Vincze, T., Fomenkov, A., Kumar, S., Too, PH-M., Gonchar, D., Degtyarev, S.K. and Roberts, R.J. (2015) Complete Genome Sequence Analysis of Bacillus Subtilis T30 Genome Announc; 3(3), e00395-15. PubMedID: 25953183
- Agrawal, A., Bisharyan, Y., Papoyan, A, Bednenko, J., Cardarelli, J., Yao, M., Clark, T., Berkmen, M., Ke, N., Colussi, P. (2019) Fusion to Tetrahymena thermophila granule lattice protein 1 confers solubility to sexual stage malaria antigens in Escherichia coli. Protein Expr Purif; 153, 7-17. PubMedID: 30081196, DOI: 10.1016/j.pep.2018.08.001.
- Anton, Brian; Roberts, Rich; Murray, Iain (2019) Complete genome sequence and methylome analysis of Micrococcus luteus SA211 a halophilic lithium-tolerant Actinobacterium from Argentina Microbiol Resour Announc; 8, 7-18. PubMedID: 30701250, DOI: 10.1128/MRA.01557-18
- Roberts, R.J., Vincze, T., Posfai, J., Macelis, D. (2014) REBASE - A database for DNA restriction and modification: enzymes, genes and genomes Nucleic Acids Res; PubMedID: 25378308
- Deptula, P., Smolander, O.-P., Laine, P., Roberts, R.J., Edelmann, M., Peltola, P., Piironen, V., Paulin, L., Storgards, E., Savijoki, K., Laitila, A., Auvinen, P., Varmanen, P (2018) Acidipropionibacterium virtanenii sp nov isolated from malted barley Int J Syst Evol Microbiol; 68, 3175-3183. PubMedID: 30156530
- Anton, B.P., Roberts, R.J., Fomenkov, A., Humbert, A., Stoian, N., Zeilstra-Ryalls, J. (2018) Complete genome sequences of two Rhodobacter strains Microbiol Resour Announc; 7 (12), e01162-18. PubMedID: 30533667
- Fomenkov, A., Vincze, T., Mersha, F., Roberts, R.J. (2018) Complete genome sequence and methylome analysis of Bacillus caldolyticus NEB414. Genome Announ.; 6 (6), e01605-17. PubMedID: 29439055 , DOI: 10.1128/genomeA.01605-17
- Bottacini, F., Morrissey, R., Roberts, R.J., James, J., van Breen, J., Egan, M., Lambert, J., van Limpt, K., Knol, J., O'Connell Motherway, M. and van Sinderen, D. (2018) Comparative genome and methylome analysis reveals restriction/modification system diversity in the gut commensal Bifidobacterium breve. Nucleic Acids Res; 46(4), 1860-1877. PubMedID: 29294107, DOI: 10.1093/nar/gkx1289
- Murray, Iain; Morgan, Rick; Luyten, Yvette; Fomenkov, Alexey; Correa, Ivan; Dai, Nan; Roberts, Rich; (2018) The non-specific adenine DNA methyltransferase M.EcoGII. Nucleic Acids Res; (2), 840-848. PubMedID: 29228259, DOI: 10.1093/nar/gkx1191
- Lim, Y.L., Roberts, R.J., Ee, R., Yin, W.F. and Chan, K.G. (2016) Complete Genome Sequence and Methylome Analysis of Aeromonas hydrophila Strain YL17, Isolated from a Compost Pile. Genome Announc; Mar 3;4(2), PubMedID: 26941143
- Yao, K., Muruvanda, T., Roberts, R.J., Payne, J., Allard, M.W. and Hoffmann, M. (2016) Complete Genome and Methylome Sequences of Salmonella enterica subsp. enterica Serovar Panama (ATCC 7378) and Salmonella enterica subsp. enterica Serovar Sloterdijk (ATCC 15791). Genome Announc; Mar 17;4(2)., PubMedID: 26988049
- Anton, B.P., Harhay, G.P., Smith, T.P., Blom, J. and Roberts, R.J. (2016) Comparative Methylome Analysis of the Occasional Ruminant Respiratory Pathogen Bibersteinia trehalosi. PLoS One; Aug 24, 11(8):e0161499.. PubMedID: 27556252
- Morgan, R.D., Luyten, Y.A., Johnson, S.A., Clough, E.M., Clark, T.A. and Roberts, R.J. (2016) Novel m4C modification in type I restriction-modification systems. Nucleic Acids Res; Nov, 2;44(19):9413-9425. PubMedID: 27580720
- Blow, M.J., Clark, T.A., Daum, C.G., Deutschbauer, A.M., Fomenkov, A., Fries, R., Froula, J., Kang, D.D., Malmstrom, R.R., Morgan, R.D., Posfai, J., Singh, K., Visel, A., Wetmore, K., Zhao, Z., Rubin, E.M., Korlach, J., Pennacchio, L.A. and Roberts, R.J. (2016) The Epigenomic Landscape of Prokaryotes. PLoS Genet; Feb 12;12(2):e1005854, PubMedID: 26870957, DOI: 10.1371/journal.pgen.1005854
- Ee, R., Lim, Y.L., Yin, W.F., See-Too, W.S., Roberts, R.J. and Chan, K.G. (2016) Novel Methyltransferase Recognition Motif Identified in Chania multitudinisentens RB-25(T) gen. nov., sp. nov. Front Microbiol; 206, 31;7:1362. PubMedID: 27630623 , DOI: 10.3389/fmicb.2016.01362
- Positive controls for methylation specific PCR or bisulfite sequencing
- CpG-methylated gene expression studies
- Nucleosome footprinting
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