Methyltransferases
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Epigenetics - Expanding on Genomic Foundations
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- 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
- 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
- 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
- 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
- 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
- Pais, J.E., Dai, N., Tamanaha, E., Vaisvila, R., Fomenkov, A.I., Bitinaite, J., Sun, Z., Guan, S., Correa, I.R. Jr., Noren, C.J., Cheng, X., Roberts, R.J., Zheng, Y. and Saleh, L. (2015) Biochemical characterization of a Naegleria TET-like oxygenase and its application in single molecule sequencing of 5-methylcytosine Proc Natl Acad Sci U S A; 112(14), 4315-4321. PubMedID: 25831492
- 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;
- 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
- 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
- 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
- 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
- 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
- Positive controls for methylation specific PCR or bisulfite sequencing
- CpG-methylated gene expression studies
- Nucleosome footprinting
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