Blumenthal, Robert M

Robert M Blumenthal
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Positions

Director, Bioinformatics-Proteomics/Genomics Program, University of Toledo , University of Toledo

Contact Info

Robert.Blumenthal@utoledo.edu

http://www.utoledo.edu/med/depts/micro/faculty/blumenthal.html

selected publications

Article (Faculty180)
- 2022
  
  Differential ETS1 binding to T:G mismatches within a CpG dinucleotide contributes to C-to-T somatic mutation rate of the IDH2 hotspot at codon Arg140. DNA repair. 113:103306.
- 2022
  
  Enzymatic Characterization of In Vitro Activity of RNA Methyltransferase PCIF1 on DNA. Biochemistry.
- 2022
  
  Enzymatic characterization of mRNA cap adenosine-N6 methyltransferase PCIF1 activity on uncapped RNAs. The Journal of biological chemistry. 298:101751.
- 2022
  
  Mediating and maintaining methylation while minimizing mutation: Recent advances on mammalian DNA methyltransferases. Current opinion in structural biology. 75:102433.
- 2021
  
  A Role for N6-Methyladenine in DNA Damage Repair. Trends in biochemical sciences. 46:175-183.
- 2021
  
  Clostridioides difficile specific DNA adenine methyltransferase CamA squeezes and flips adenine out of DNA helix. Nature communications. 12:3436.
- 2021
  
  Human MettL3-MettL14 RNA adenine methyltransferase complex is active on double-stranded DNA containing lesions. Nucleic acids research. 49:11629-11642.
- 2021
  
  Preferential CEBP binding to T:G mismatches and increased C-to-T human somatic mutations. Nucleic acids research. 49:5084-5094.
- 2021
  
  Repurposing epigenetic inhibitors to target the specific DNA adenine methyltransferase and sporulation regulator CamA. Epigenetics. 1-12.
- 2020
  
  Beta class amino methyltransferases from bacteria to humans: evolution and structural consequences. Nucleic acids research. 48:10034-10044.
- 2020
  
  Biochemical and structural basis for YTH domain of human YTHDC1 binding to methylated adenine in DNA. Nucleic acids research. 48:10329-10341.
- 2020
  
  Distribution of RecBCD and AddAB recombination-associated genes among bacteria in 33 phyla. Microbiology (Reading, England). 166:1047-1064.
- 2019
  
  Detection of DNA Modifications by Sequence-Specific Transcription Factors. Journal of molecular biology.
- 2019
  
  Structural basis for effects of CpA modifications on C/EBPβ binding of DNA. Nucleic acids research. 47:1774-1785.
- 2019
  
  Structural basis for preferential binding of human TCF4 to DNA containing 5-carboxylcytosine. Nucleic acids research. 47:8375-8387.
- 2018
  
  Detecting and interpreting DNA methylation marks. Current opinion in structural biology. 53:88-99.
- 2018
  
  Role for first zinc finger of WT1 in DNA sequence specificity: Denys-Drash syndrome-associated WT1 mutant in ZF1 enhances affinity for a subset of WT1 binding sites. Nucleic acids research. 46:3864-3877.
- 2017
  
  Complementation of a metK-deficient E. coli strain with heterologous AdoMet synthetase genes. Microbiology (Reading, England). 163:1812-1821.
- 2017
  
  Methyl-dependent and spatial-specific DNA recognition by the orthologous transcription factors human AP-1 and Epstein-Barr virus Zta. Nucleic acids research. 45:2503-2515.
- 2017
  
  Structural basis of human PR/SET domain 9 (PRDM9) allele C-specific recognition of its cognate DNA sequence. The Journal of biological chemistry. 292:15994-16002.
- 2016
  
  Distinctive Klf4 mutants determine preference for DNA methylation status. Nucleic acids research. 44:10177-10185.
- 2016
  
  Evolution of a global regulator: Lrp in four orders of γ-Proteobacteria. BMC evolutionary biology. 16:111.
- 2015
  
  A surprising range of modified-methionyl S-adenosylmethionine analogues support bacterial growth. Microbiology (Reading, England). 161:674-82.
- 2015
  
  Structures of Escherichia coli DNA adenine methyltransferase (Dam) in complex with a non-GATC sequence: potential implications for methylation-independent transcriptional repression. Nucleic acids research. 43:4296-308.
- 2014
  
  Producing proficient methyl donors from alternative substrates of S-adenosylmethionine synthetase. Biochemistry. 53:1521-6.
- 2014
  
  Structural basis for Klf4 recognition of methylated DNA. Nucleic acids research. 42:4859-67.
- 2013
  
  A bistable hysteretic switch in an activator-repressor regulated restriction-modification system. Nucleic acids research. 41:6045-57.
- 2013
  
  A common mode of recognition for methylated CpG. Trends in biochemical sciences. 38:177-83.
- 2013
  
  Emergence, origin, and function of neutrophil-dendritic cell hybrids in experimentally induced inflammatory lesions in mice. Blood. 121:1690-700.
- 2013
  
  Naturally-occurring, dually-functional fusions between restriction endonucleases and regulatory proteins. BMC evolutionary biology. 13:218.
- 2013
  
  Response to mackay et Al. Trends in biochemical sciences. 38:423.
- 2013
  
  The COMBREX project: design, methodology, and initial results. PLoS biology. 11:e1001638.
- 2011
  
  Higher incidence of perineal community acquired MRSA infections among toddlers. BMC pediatrics. 11:96.
- 2011
  
  Introduction--Epiphanies in epigenetics. Progress in molecular biology and translational science. 101:1-21.
- 2011
  
  We would like to thank those who made this volume possible. Preface. Progress in molecular biology and translational science. 101:xiii-xiv.
- 2010
  
  Coordinated chromatin control: structural and functional linkage of DNA and histone methylation. Biochemistry. 49:2999-3008.
- 2010
  
  Translational independence between overlapping genes for a restriction endonuclease and its transcriptional regulator. BMC molecular biology. 11:87.
- 2009
  
  Tuning the relative affinities for activating and repressing operators of a temporally regulated restriction-modification system. Nucleic acids research. 37:983-98.
- 2008
  
  Limited functional conservation of a global regulator among related bacterial genera: Lrp in Escherichia, Proteus and Vibrio. BMC microbiology. 8:60.
- 2008
  
  Mammalian DNA methyltransferases: a structural perspective. Structure (London, England : 1993). 16:341-50.
- 2008
  
  Real-time kinetics of restriction-modification gene expression after entry into a new host cell. Nucleic acids research. 36:2581-93.
- 2007
  
  Integration of regulatory signals through involvement of multiple global regulators: control of the Escherichia coli gltBDF operon by Lrp, IHF, Crp, and ArgR. BMC microbiology. 7:2.
- 2007
  
  Regulatory circuit based on autogenous activation-repression: roles of C-boxes and spacer sequences in control of the PvuII restriction-modification system. Nucleic acids research. 35:6935-52.
- 2006
  
  1 Protein Methyltransferases: Their Distribution Among the Five Structural Classes of AdoMet-Dependent Methyltransferases. The Enzymes. 24:3-28.
- 2005
  
  Nature of the promoter activated by C.PvuII, an unusual regulatory protein conserved among restriction-modification systems. Journal of bacteriology. 187:488-97.
- 2003
  
  A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. Nucleic acids research. 31:1805-12.
- 2003
  
  Many paths to methyltransfer: a chronicle of convergence. Trends in biochemical sciences. 28:329-35.
- 2002
  
  Mobility of a restriction-modification system revealed by its genetic contexts in three hosts. Journal of bacteriology. 184:2411-9.
- 2000
  
  Recognition of native DNA methylation by the PvuII restriction endonuclease. Nucleic acids research. 28:3143-50.
- 1999
  
  Substrate recognition by the Pvu II endonuclease: binding and cleavage of CAG5mCTG sites. Nucleic acids research. 27:1032-8.
- 1997
  
  A genetic and functional analysis of the unusually large variable region in the M.AluI DNA-(cytosine C5)-methyltransferase. Molecular & general genetics : MGG. 257:14-22.
- 1997
  
  The PvuII DNA (cytosine-N4)-methyltransferase comprises two trypsin-defined domains, each of which binds a molecule of S-adenosyl-L-methionine. Biochemistry. 36:8284-92.
- 1997
  
  Use of an inducible regulatory protein to identify members of a regulon: application to the regulon controlled by the leucine-responsive regulatory protein (Lrp) in Escherichia coli. Journal of bacteriology. 179:6254-63.
- 1996
  
  Experimental analysis of global gene regulation in Escherichia coli. Progress in nucleic acid research and molecular biology. 55:1-86.
- 1995
  
  Characterization of pPvu1, the autonomous plasmid from Proteus vulgaris that carries the genes of the PvuII restriction-modification system. Gene. 157:73-9.
- 1995
  
  Gene pvuIIW: a possible modulator of PvuII endonuclease subunit association. Gene. 157:193-9.
- 1993
  
  Assignment of enzymatic function to specific protein regions of cobalamin-dependent methionine synthase from Escherichia coli. Biochemistry. 32:9290-5.
- 1993
  
  Regulation of the gltBDF operon of Escherichia coli: how is a leucine-insensitive operon regulated by the leucine-responsive regulatory protein?. Journal of bacteriology. 175:7160-9.
- 1993
  
  The M.AluI DNA-(cytosine C5)-methyltransferase has an unusually large, partially dispensable, variable region. Nucleic acids research. 21:905-11.
- 1992
  
  Analysis of macromolecular biosynthesis to define the quinolone-induced postantibiotic effect in Escherichia coli. Antimicrobial agents and chemotherapy. 36:2118-24.
- 1992
  
  Sequence and characterization of pvuIIR, the PvuII endonuclease gene, and of pvuIIC, its regulatory gene. Journal of bacteriology. 174:3395-8.
- 1991
  
  A family of regulatory genes associated with type II restriction-modification systems. Journal of bacteriology. 173:1367-75.
- 1989
  
  Sequence, internal homology and high-level expression of the gene for a DNA-(cytosine N4)-methyltransferase, M.Pvu II. Nucleic acids research. 17:4161-75.
- 1988
  
  Isolation of mutants in a DNA methyltransferase through mcrB-mediated restriction. Gene. 74:271-3.
- 1988
  
  McrA and McrB restriction phenotypes of some E. coli strains and implications for gene cloning. Nucleic acids research. 16:1563-75.
- 1988
  
  Nomenclature for bacterial genes coding for class-II restriction endonucleases and modification methyltransferases. Gene. 74:279-80.
- 1987
  
  The Pvu II restriction-modification system: cloning, characterization and use in revealing an E. coli barrier to certain methylases or methylated DNAs. Gene amplification and analysis. 5:227-45.
- 1985
  
  Cloning of a restriction-modification system from Proteus vulgaris and its use in analyzing a methylase-sensitive phenotype in Escherichia coli. Journal of bacteriology. 164:501-9.
- 1983
  
  Occurrence and expression of imipemide (N-formimidoyl thienamycin) resistance in clinical isolates of coagulase-negative staphylococci. Antimicrobial agents and chemotherapy. 24:61-9.
- 1983
  
  The isolation and characterization of the Escherichia coli DNA adenine methylase (dam) gene. Nucleic acids research. 11:837-51.
- 1982
  
  Computer programs for nucleic acid sequence manipulation. Nucleic acids research. 10:91-101.
- 1981
  
  Bovine rotavirus-cell interactions: effect of virus infection on cellular integrity and macromolecular synthesis. Virology. 114:86-97.
- 1981
  
  Proteins Specified by bovine herpesvirus 1 (infectious bovine rhinotracheitis virus). Journal of virology. 40:367-78.
- 1980
  
  Gene expression in Escherichia coli after amino acid, purine, or pyrimidine exhaustion. Journal of bacteriology. 142:202-11.
- 1980
  
  Regulation of ribonucleic acid polymerase synthesis during restriction of an Escherichia coli mutant temperature sensitive for transcription factor sigma. Journal of bacteriology. 142:1049-54.
- 1978
  
  Gene expression in Escherichia coli B/r during partial rifampicin-mediated restrictions of transcription initiation. Molecular & general genetics : MGG. 165:79-86.
- 1976
  
  A mutant of Escherichia coli with an altered elongation factor Tu. Proceedings of the National Academy of Sciences of the United States of America. 73:1698-701.
- 1976
  
  Regulation of transcription factor rho and the alpha subunit of RNA polymerase in Escherichia coli B/r. Proceedings of the National Academy of Sciences of the United States of America. 73:2285-8.
- 1976
  
  The effects of the relA gene on the synthesis of aminoacyl-tRNA synthetases and other transcription and translation proteins in Escherichia coli A. Molecular & general genetics : MGG. 149:291-6.
- Enzymatic characterization of three human RNA adenosine methyltransferases reveals diverse substrate affinities and reaction optima. The Journal of biological chemistry. 296:100270.
Article (Web of Science)
- 2021
  
  Preferential CEBP binding to T:G mismatches and increased C-to-T human somatic mutations. NUCLEIC ACIDS RESEARCH. 49:5084-5094.
  Full Text via DOI: 10.1093/nar/gkab276 PMID: 33877329
- 2020
  
  Distribution of RecBCD and AddAB recombination-associated genes among bacteria in 33 phyla. MICROBIOLOGY-SGM. 166:1047-1064.
  Full Text via DOI: 10.1099/mic.0.000980 PMID: 33085588
- 2020
  
  Beta class amino methyltransferases from bacteria to humans: evolution and structural consequences. NUCLEIC ACIDS RESEARCH. 48:10034-10044.
  Full Text via DOI: 10.1093/nar/gkaa446 PMID: 32453412
- 2020
  
  Biochemical and structural basis for YTH domain of human YTHDC1 binding to methylated adenine in DNA. NUCLEIC ACIDS RESEARCH. 48:10329-10341.
  Full Text via DOI: 10.1093/nar/gkaa604 PMID: 32663306
- 2019
  
  Structural basis for preferential binding of human TCF4 to DNA containing 5-carboxylcytosine. NUCLEIC ACIDS RESEARCH. 47:8375-8387.
  Full Text via DOI: 10.1093/nar/gkz381 PMID: 31081034
- 2019
  
  Structural basis for effects of CpA modifications on C/EBP binding of DNA. NUCLEIC ACIDS RESEARCH. 47:1774-1785.
  Full Text via DOI: 10.1093/nar/gky1264 PMID: 30566668
- 2018
  
  Detecting and interpreting DNA methylation marks. CURRENT OPINION IN STRUCTURAL BIOLOGY. 53:88-99.
  Full Text via DOI: 10.1016/j.sbi.2018.06.004
- 2018
  
  Role for first zinc finger of WT1 in DNA sequence specificity: Denys-Drash syndrome-associated WT1 mutant in ZF1 enhances affinity for a subset of WT1 binding sites. NUCLEIC ACIDS RESEARCH. 46:3864-3877.
  Full Text via DOI: 10.1093/nar/gkx1274
- 2017
  
  Complementation of a metK-deficient E. coli strain with heterologous AdoMet synthetase genes. MICROBIOLOGY-SGM. 163:1812-1821.
  Full Text via DOI: 10.1099/mic.0.000565
- 2017
  
  Structural basis of human PR/SET domain 9 (PRDM9) allele C-specific recognition of its cognate DNA sequence. JOURNAL OF BIOLOGICAL CHEMISTRY. 292:15994-16002.
  Full Text via DOI: 10.1074/jbc.M117.805754
- 2017
  
  Methyl-dependent and spatial-specific DNA recognition by the orthologous transcription factors human AP-1 and Epstein-Barr virus Zta. NUCLEIC ACIDS RESEARCH. 45:2503-2515.
  Full Text via DOI: 10.1093/nar/gkx057
- 2017
  
  Structural basis of human PR/SET domain 9 (PRDM9) allele C–specific recognition of its cognate DNA sequence. JOURNAL OF BIOLOGICAL CHEMISTRY. 292:15994-16002.
  Full Text via DOI: 10.1074/jbc.m117.805754
- 2016
  
  Distinctive Klf4 mutants determine preference for DNA methylation status. NUCLEIC ACIDS RESEARCH. 44:10177-10185.
  Full Text via DOI: 10.1093/nar/gkw774
- 2016
  
  Evolution of a global regulator: Lrp in four orders of gamma-Proteobacteria. BMC EVOLUTIONARY BIOLOGY. 16.
  Full Text via DOI: 10.1186/s12862-016-0685-1
- 2015
  
  Structures of Escherichia coli DNA adenine methyltransferase (Dam) in complex with a non-GATC sequence: potential implications for methylation-independent transcriptional repression. NUCLEIC ACIDS RESEARCH. 43:4296-4308.
  Full Text via DOI: 10.1093/nar/gkv251
- 2015
  
  A surprising range of modified-methionyl S-adenosylmethionine analogues support bacterial growth. MICROBIOLOGY-SGM. 161:674-682.
  Full Text via DOI: 10.1099/mic.0.000034
- 2014
  
  Structural basis for Klf4 recognition of methylated DNA. NUCLEIC ACIDS RESEARCH. 42:4859-4867.
  Full Text via DOI: 10.1093/nar/gku134
- 2014
  
  Producing Proficient Methyl Donors from Alternative Substrates of S-Adenosylmethionine Synthetase. BIOCHEMISTRY. 53:1521-1526.
  Full Text via DOI: 10.1021/bi401556p
- 2013
  
  Naturally-occurring, dually-functional fusions between restriction endonucleases and regulatory proteins. BMC EVOLUTIONARY BIOLOGY. 13.
  Full Text via DOI: 10.1186/1471-2148-13-218
- 2013
  
  A bistable hysteretic switch in an activator-repressor regulated restriction-modification system. NUCLEIC ACIDS RESEARCH. 41:6045-6057.
  Full Text via DOI: 10.1093/nar/gkt324
- 2013
  
  Emergence, origin, and function of neutrophil-dendritic cell hybrids in experimentally induced inflammatory lesions in mice. BLOOD. 121:1690-1700.
  Full Text via DOI: 10.1182/blood-2012-07-445197
- 2011
  
  Higher incidence of perineal community acquired MRSA infections among toddlers. BMC PEDIATRICS. 11.
  Full Text via DOI: 10.1186/1471-2431-11-96
- 2011
  
  Recognition of DNA by the Helix-Turn-Helix Global Regulatory Protein Lrp Is Modulated by the Amino Terminus. JOURNAL OF BACTERIOLOGY. 193:3794-3803.
  Full Text via DOI: 10.1128/JB.00191-11
- 2011
  
  Recognition of DNA by the Helix-Turn-Helix Global Regulatory Protein Lrp Is Modulated by the Amino Terminus. JOURNAL OF BACTERIOLOGY. 193:3794-3803.
  Full Text via DOI: 10.1128/jb.00191-11
- 2010
  
  Translational independence between overlapping genes for a restriction endonuclease and its transcriptional regulator. BMC MOLECULAR BIOLOGY. 11.
  Full Text via DOI: 10.1186/1471-2199-11-87
- 2010
  
  Coordinated Chromatin Control: Structural and Functional Linkage of DNA and Histone Methylation. BIOCHEMISTRY. 49:2999-3008.
  Full Text via DOI: 10.1021/bi100213t
- 2009
  
  Tuning the relative affinities for activating and repressing operators of a temporally regulated restriction-modification system. NUCLEIC ACIDS RESEARCH. 37:983-998.
  Full Text via DOI: 10.1093/nar/gkn1010
- 2008
  
  Real-time kinetics of restrictionmodification gene expression after entry into a new host cell. NUCLEIC ACIDS RESEARCH. 36:2581-2593.
  Full Text via DOI: 10.1093/nar/gkn097
- 2007
  
  Regulatory circuit based on autogenous activation-repression: roles of C-boxes and spacer sequences in control of the PvuII restriction-modification system. NUCLEIC ACIDS RESEARCH. 35:6935-6952.
  Full Text via DOI: 10.1093/nar/gkm837
- 2007
  
  Integration of regulatory signals through involvement of multiple global regulators: control of the Escherichia coli gltBDF operon by Lrp, IHF, Crp, and ArgR. BMC MICROBIOLOGY. 7.
  Full Text via DOI: 10.1186/1471-2180-7-2
Book Chapter (Web of Science)
- 2011
  
  Introduction-Epiphanies in Epigenetics. MODIFICATIONS OF NUCLEAR DNA AND ITS REGULATORY PROTEINS. 1-21.
  Full Text via DOI: 10.1016/B978-0-12-387685-0.00001-9
- 2011
  
  Introduction—Epiphanies in Epigenetics. Progress in Molecular Biology and Translational Science. 1-21.
  Full Text via DOI: 10.1016/b978-0-12-387685-0.00001-9
Editorial Material (Web of Science)
- 2013
  
  The COMBREX Project: Design, Methodology, and Initial Results. PLOS BIOLOGY.
  Full Text via DOI: 10.1371/journal.pbio.1001638
Letter (Web of Science)
- 2013
  
  Is there a telltale RH fingerprint in zinc fingers that recognizes methylated CpG dinucleotides? Response. TRENDS IN BIOCHEMICAL SCIENCES. 423-423.
  Full Text via DOI: 10.1016/j.tibs.2013.06.010
Meeting Abstract (Web of Science)
- 2017
  
  Growth based complementation assay in E. coli for inhibitor screening of S-adenosylmethionine synthetase. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY.
- 2017
  
  A cell-based inhibitor screening platform for S-adenosylmethionine synthetase. FASEB JOURNAL.
- 2016
  
  Targeting bacterial virulence through alternative substrates of S-adenosylmethionine synthetase. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY.
Review Article (Web of Science)
- 2021
  
  A Role for N6-Methyladenlne in DNA Damage Repair. TRENDS IN BIOCHEMICAL SCIENCES. 175-183.
  Full Text via DOI: 10.1016/j.tibs.2020.09.007 PMID: 33077363
- 2020
  
  Detection of DNA Modifications by Sequence-Specific Transcription Factors. JOURNAL OF MOLECULAR BIOLOGY. 1661-1673.
  Full Text via DOI: 10.1016/j.jmb.2019.09.013 PMID: 31626807
- 2013
  
  A common mode of recognition for methylated CpG. TRENDS IN BIOCHEMICAL SCIENCES. 177-183.
  Full Text via DOI: 10.1016/j.tibs.2012.12.005
- 2008
  
  Limited functional conservation of a global regulator among related bacterial genera: Lrp in Escherichia, Proteus and Vibrio. BMC MICROBIOLOGY.
  Full Text via DOI: 10.1186/1471-2180-8-60
- 2008
  
  Mammalian DNA methyltransferases: A structural perspective. STRUCTURE. 341-350.
  Full Text via DOI: 10.1016/j.str.2008.01.004

full name

Robert M Blumenthal

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